Starting phenix.real_space_refine on Mon Feb 19 11:14:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvz_27022/02_2024/8cvz_27022.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvz_27022/02_2024/8cvz_27022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvz_27022/02_2024/8cvz_27022.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvz_27022/02_2024/8cvz_27022.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvz_27022/02_2024/8cvz_27022.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvz_27022/02_2024/8cvz_27022.pdb" } resolution = 3.52 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= 0.101 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: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 15760 2.51 5 N 4173 2.21 5 O 4465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 52": "OE1" <-> "OE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ASP 163": "OD1" <-> "OD2" Residue "J PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 178": "OD1" <-> "OD2" Residue "J ARG 180": "NH1" <-> "NH2" Residue "J TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 321": "OD1" <-> "OD2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B GLU 590": "OE1" <-> "OE2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C ARG 472": "NH1" <-> "NH2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C GLU 539": "OE1" <-> "OE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 624": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D ASP 135": "OD1" <-> "OD2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 275": "OD1" <-> "OD2" Residue "D PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 303": "NH1" <-> "NH2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "D ASP 561": "OD1" <-> "OD2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 321": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "I PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 178": "OD1" <-> "OD2" Residue "I ARG 180": "NH1" <-> "NH2" Residue "I TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24517 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4808 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4781 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 575} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4777 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 24, 'TRANS': 576} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4834 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 576} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 295 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "I" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2100 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 253} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 295 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 12.09, per 1000 atoms: 0.49 Number of scatterers: 24517 At special positions: 0 Unit cell: (125.245, 134.387, 160.899, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 4465 8.00 N 4173 7.00 C 15760 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: 10.20 Conformation dependent library (CDL) restraints added in 4.3 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 21 sheets defined 54.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'J' and resid 13 through 29 removed outlier: 3.754A pdb=" N GLY J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 53 removed outlier: 3.664A pdb=" N THR J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'J' and resid 111 through 117 Processing helix chain 'J' and resid 142 through 156 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.503A pdb=" N ILE J 166 " --> pdb=" O GLY J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 176 Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 197 through 205 removed outlier: 3.653A pdb=" N PHE J 201 " --> pdb=" O TYR J 197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 203 " --> pdb=" O PRO J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 257 removed outlier: 3.595A pdb=" N ILE J 252 " --> pdb=" O LEU J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.826A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.526A pdb=" N LYS B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 145 through 169 Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.977A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 removed outlier: 3.814A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.310A pdb=" N LEU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.859A pdb=" N GLN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.899A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 616 removed outlier: 4.281A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 616 " --> pdb=" O ALA B 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.359A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 121 through 138 removed outlier: 3.984A pdb=" N ALA C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 168 Processing helix chain 'C' and resid 181 through 194 removed outlier: 4.139A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 4.089A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 295 through 313 Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.666A pdb=" N PHE C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.693A pdb=" N GLY C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 513 through 522 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 578 through 590 Processing helix chain 'C' and resid 591 through 592 No H-bonds generated for 'chain 'C' and resid 591 through 592' Processing helix chain 'C' and resid 593 through 596 Processing helix chain 'C' and resid 597 through 617 Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.885A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 77 removed outlier: 3.526A pdb=" N VAL D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.779A pdb=" N LYS D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.403A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 145 through 169 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.985A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.652A pdb=" N ARG D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 294 through 313 Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.586A pdb=" N PHE D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 411 Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.138A pdb=" N LEU D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.516A pdb=" N MET D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 498 Processing helix chain 'D' and resid 513 through 522 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.892A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 616 removed outlier: 4.531A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.824A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.521A pdb=" N LYS A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.978A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.761A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.835A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.342A pdb=" N LEU A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.905A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.300A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 327 removed outlier: 3.604A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'I' and resid 13 through 29 removed outlier: 3.751A pdb=" N GLY I 18 " --> pdb=" O ALA I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 removed outlier: 3.626A pdb=" N VAL I 50 " --> pdb=" O SER I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 80 through 88 removed outlier: 3.558A pdb=" N HIS I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 142 through 156 Processing helix chain 'I' and resid 162 through 171 Processing helix chain 'I' and resid 172 through 176 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 191 through 197 Processing helix chain 'I' and resid 197 through 205 removed outlier: 3.723A pdb=" N PHE I 201 " --> pdb=" O TYR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 222 Processing helix chain 'I' and resid 238 through 242 removed outlier: 3.534A pdb=" N HIS I 242 " --> pdb=" O ASN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 257 removed outlier: 3.588A pdb=" N ILE I 252 " --> pdb=" O LEU I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 264 Processing helix chain 'F' and resid 318 through 327 removed outlier: 3.725A pdb=" N LYS F 322 " --> pdb=" O SER F 318 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'G' and resid 318 through 327 removed outlier: 3.723A pdb=" N LYS G 322 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU G 323 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'H' and resid 318 through 327 removed outlier: 3.724A pdb=" N LYS H 322 " --> pdb=" O SER H 318 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU H 323 " --> pdb=" O GLU H 319 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 removed outlier: 4.113A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 57 through 60 removed outlier: 7.041A pdb=" N GLN J 4 " --> pdb=" O ARG J 34 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL J 36 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE J 6 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU J 38 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR J 8 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU J 9 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL J 136 " --> pdb=" O ALA J 123 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA J 123 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 105 through 107 removed outlier: 3.705A pdb=" N HIS J 212 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.300A pdb=" N TYR B 62 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL B 115 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE B 255 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.543A pdb=" N VAL B 362 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 476 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA B 364 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 374 through 375 removed outlier: 3.936A pdb=" N ASN B 374 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.654A pdb=" N VAL C 28 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS C 178 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 175 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE C 201 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA C 177 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 67 removed outlier: 6.580A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.713A pdb=" N THR C 257 " --> pdb=" O ILE C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 475 removed outlier: 6.535A pdb=" N VAL C 362 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 372 through 375 removed outlier: 4.146A pdb=" N ASN C 374 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 62 through 63 removed outlier: 8.525A pdb=" N PHE D 63 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 175 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 201 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 257 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 478 removed outlier: 6.546A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE D 476 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA D 364 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS D 478 " --> pdb=" O ALA D 364 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE D 366 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N PHE D 505 " --> pdb=" O THR D 529 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 372 through 375 removed outlier: 7.032A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.302A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 255 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.547A pdb=" N VAL A 362 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 476 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA A 364 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.565A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.636A pdb=" N ILE I 59 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS I 97 " --> pdb=" O ASP I 3 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU I 9 " --> pdb=" O MET I 101 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL I 136 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA I 123 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER I 121 " --> pdb=" O VAL I 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 105 through 107 removed outlier: 6.287A pdb=" N LEU I 189 " --> pdb=" O HIS I 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 224 through 225 1169 hydrogen bonds defined for protein. 3402 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: 9.63 Time building geometry restraints manager: 11.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4241 1.32 - 1.45: 7485 1.45 - 1.58: 13252 1.58 - 1.71: 0 1.71 - 1.85: 180 Bond restraints: 25158 Sorted by residual: bond pdb=" CE1 HIS C 311 " pdb=" NE2 HIS C 311 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" CA ALA B 37 " pdb=" CB ALA B 37 " ideal model delta sigma weight residual 1.537 1.484 0.053 1.38e-02 5.25e+03 1.49e+01 bond pdb=" C VAL C 32 " pdb=" O VAL C 32 " ideal model delta sigma weight residual 1.238 1.197 0.040 1.06e-02 8.90e+03 1.43e+01 bond pdb=" CA SER D 169 " pdb=" CB SER D 169 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.26e-02 6.30e+03 1.37e+01 bond pdb=" CA SER C 528 " pdb=" CB SER C 528 " ideal model delta sigma weight residual 1.527 1.473 0.054 1.49e-02 4.50e+03 1.33e+01 ... (remaining 25153 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.63: 418 104.63 - 112.18: 9853 112.18 - 119.74: 12116 119.74 - 127.29: 11505 127.29 - 134.85: 259 Bond angle restraints: 34151 Sorted by residual: angle pdb=" C PRO D 112 " pdb=" CA PRO D 112 " pdb=" CB PRO D 112 " ideal model delta sigma weight residual 111.46 100.37 11.09 1.21e+00 6.83e-01 8.41e+01 angle pdb=" C THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta sigma weight residual 109.24 124.32 -15.08 1.75e+00 3.27e-01 7.43e+01 angle pdb=" C THR B 49 " pdb=" CA THR B 49 " pdb=" CB THR B 49 " ideal model delta sigma weight residual 109.24 123.83 -14.59 1.75e+00 3.27e-01 6.95e+01 angle pdb=" C THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta sigma weight residual 109.24 123.61 -14.37 1.75e+00 3.27e-01 6.74e+01 angle pdb=" C PRO C 506 " pdb=" CA PRO C 506 " pdb=" CB PRO C 506 " ideal model delta sigma weight residual 111.11 101.99 9.12 1.17e+00 7.31e-01 6.08e+01 ... (remaining 34146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13178 17.89 - 35.78: 1183 35.78 - 53.67: 323 53.67 - 71.56: 52 71.56 - 89.45: 6 Dihedral angle restraints: 14742 sinusoidal: 5796 harmonic: 8946 Sorted by residual: dihedral pdb=" C THR A 49 " pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta harmonic sigma weight residual -122.00 -143.81 21.81 0 2.50e+00 1.60e-01 7.61e+01 dihedral pdb=" C THR B 49 " pdb=" N THR B 49 " pdb=" CA THR B 49 " pdb=" CB THR B 49 " ideal model delta harmonic sigma weight residual -122.00 -143.32 21.32 0 2.50e+00 1.60e-01 7.27e+01 dihedral pdb=" C THR D 49 " pdb=" N THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta harmonic sigma weight residual -122.00 -143.28 21.28 0 2.50e+00 1.60e-01 7.25e+01 ... (remaining 14739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2992 0.160 - 0.320: 649 0.320 - 0.480: 71 0.480 - 0.640: 5 0.640 - 0.799: 3 Chirality restraints: 3720 Sorted by residual: chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA THR D 49 " pdb=" N THR D 49 " pdb=" C THR D 49 " pdb=" CB THR D 49 " both_signs ideal model delta sigma weight residual False 2.53 1.74 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA THR B 49 " pdb=" N THR B 49 " pdb=" C THR B 49 " pdb=" CB THR B 49 " both_signs ideal model delta sigma weight residual False 2.53 1.74 0.78 2.00e-01 2.50e+01 1.53e+01 ... (remaining 3717 not shown) Planarity restraints: 4381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 572 " -0.079 2.00e-02 2.50e+03 4.27e-02 3.64e+01 pdb=" CG TYR C 572 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR C 572 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 572 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 572 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 572 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 572 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 572 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 62 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C TYR C 62 " -0.093 2.00e-02 2.50e+03 pdb=" O TYR C 62 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE C 63 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 154 " 0.023 2.00e-02 2.50e+03 3.84e-02 2.58e+01 pdb=" CG PHE B 154 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE B 154 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE B 154 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 154 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 154 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE B 154 " -0.022 2.00e-02 2.50e+03 ... (remaining 4378 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 366 2.67 - 3.23: 23177 3.23 - 3.79: 40442 3.79 - 4.34: 56360 4.34 - 4.90: 88834 Nonbonded interactions: 209179 Sorted by model distance: nonbonded pdb=" O THR C 204 " pdb=" OG1 THR C 204 " model vdw 2.118 2.440 nonbonded pdb=" N VAL B 32 " pdb=" O HIS B 178 " model vdw 2.316 2.520 nonbonded pdb=" OG1 THR D 361 " pdb=" NH2 ARG D 472 " model vdw 2.337 2.520 nonbonded pdb=" O PHE B 30 " pdb=" N HIS B 178 " model vdw 2.373 2.520 nonbonded pdb=" N PHE B 30 " pdb=" O VAL B 176 " model vdw 2.413 2.520 ... (remaining 209174 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 22 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 69 or (resid 70 and ( \ name N or name CA or name C or name O or name CB )) or resid 71 through 73 or (r \ esid 74 and (name N or name CA or name C or name O or name CB )) or resid 75 thr \ ough 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) \ or resid 110 through 126 or (resid 127 through 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 131 or (resid 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 143 or (resid 1 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 145 through \ 175 or (resid 176 through 177 and (name N or name CA or name C or name O or nam \ e CB )) or resid 178 through 180 or (resid 181 and (name N or name CA or name C \ or name O or name CB )) or resid 182 through 194 or (resid 195 and (name N or na \ me CA or name C or name O or name CB )) or resid 196 through 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 236 \ or (resid 237 and (name N or name CA or name C or name O or name CB )) or resid \ 238 through 252 or (resid 253 and (name N or name CA or name C or name O or nam \ e CB )) or resid 254 through 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 284 or (resid 285 through 286 and ( \ name N or name CA or name C or name O or name CB )) or resid 287 or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5 through 302 or (resid 303 and (name N or name CA or name C or name O or name C \ B )) or resid 304 through 332 or (resid 333 and (name N or name CA or name C or \ name O or name CB )) or resid 334 through 339 or (resid 340 and (name N or name \ CA or name C or name O or name CB )) or resid 341 through 370 or (resid 371 and \ (name N or name CA or name C or name O or name CB )) or resid 372 through 405 or \ (resid 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 414 or (resid 415 through 418 and (name N or name CA or name C or name \ O or name CB )) or resid 419 through 420 or (resid 421 through 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 429 or (resid \ 430 through 431 and (name N or name CA or name C or name O or name CB )) or resi \ d 432 through 436 or (resid 437 and (name N or name CA or name C or name O or na \ me CB )) or resid 438 through 446 or (resid 447 through 448 and (name N or name \ CA or name C or name O or name CB )) or resid 449 through 480 or (resid 481 and \ (name N or name CA or name C or name O or name CB )) or resid 482 through 509 or \ (resid 510 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 1 through 590 or (resid 591 and (name N or name CA or name C or name O or name C \ B )) or resid 592 through 596 or (resid 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 605 or (resid 606 and (name N or name \ CA or name C or name O or name CB )) or resid 607 through 608 or (resid 609 and \ (name N or name CA or name C or name O or name CB )) or resid 610 through 621 or \ (resid 622 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 3 through 626)) selection = (chain 'B' and (resid 22 through 55 or (resid 56 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 59 or (resid 60 and (na \ me N or name CA or name C or name O or name CB )) or resid 61 through 69 or (res \ id 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throu \ gh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or r \ esid 75 through 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB )) or resid 110 through 126 or (resid 127 through 128 and (name N or nam \ e CA or name C or name O or name CB )) or resid 129 through 131 or (resid 132 an \ d (name N or name CA or name C or name O or name CB )) or resid 133 through 143 \ or (resid 144 and (name N or name CA or name C or name O or name CB )) or resid \ 145 through 180 or (resid 181 and (name N or name CA or name C or name O or name \ CB )) or resid 182 through 194 or (resid 195 and (name N or name CA or name C o \ r name O or name CB )) or resid 196 through 230 or (resid 231 and (name N or nam \ e CA or name C or name O or name CB )) or resid 232 through 236 or (resid 237 an \ d (name N or name CA or name C or name O or name CB )) or resid 238 through 252 \ or (resid 253 and (name N or name CA or name C or name O or name CB )) or resid \ 254 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 284 or (resid 285 through 286 and (name N or name CA \ or name C or name O or name CB )) or resid 287 or resid 293 or (resid 294 and ( \ name N or name CA or name C or name O or name CB )) or resid 295 through 339 or \ (resid 340 and (name N or name CA or name C or name O or name CB )) or resid 341 \ through 370 or (resid 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 405 or (resid 406 and (name N or name CA or name C or n \ ame O or name CB )) or resid 407 through 415 or (resid 416 through 418 and (name \ N or name CA or name C or name O or name CB )) or resid 419 through 420 or (res \ id 421 through 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 447 or (resid 448 and (name N or name CA or name C or name O or \ name CB )) or resid 449 through 480 or (resid 481 and (name N or name CA or nam \ e C or name O or name CB )) or resid 482 through 590 or (resid 591 and (name N o \ r name CA or name C or name O or name CB )) or resid 592 through 596 or (resid 5 \ 97 and (name N or name CA or name C or name O or name CB )) or resid 598 through \ 626)) selection = (chain 'C' and (resid 22 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 55 or (resid 56 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 69 or (res \ id 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throu \ gh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or r \ esid 75 through 126 or (resid 127 through 128 and (name N or name CA or name C o \ r name O or name CB )) or resid 129 through 131 or (resid 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 175 or (resid 176 th \ rough 177 and (name N or name CA or name C or name O or name CB )) or resid 178 \ through 194 or (resid 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 259 or (resid 260 and (name N or name CA or name C or na \ me O or name CB )) or resid 261 through 284 or (resid 285 through 286 and (name \ N or name CA or name C or name O or name CB )) or resid 287 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thro \ ugh 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) o \ r resid 334 through 414 or (resid 415 through 418 and (name N or name CA or name \ C or name O or name CB )) or resid 419 through 429 or (resid 430 through 431 an \ d (name N or name CA or name C or name O or name CB )) or resid 432 through 436 \ or (resid 437 and (name N or name CA or name C or name O or name CB )) or resid \ 438 through 446 or (resid 447 through 448 and (name N or name CA or name C or na \ me O or name CB )) or resid 449 through 509 or (resid 510 and (name N or name CA \ or name C or name O or name CB )) or resid 511 through 590 or (resid 591 and (n \ ame N or name CA or name C or name O or name CB )) or resid 592 through 596 or ( \ resid 597 and (name N or name CA or name C or name O or name CB )) or resid 598 \ through 605 or (resid 606 and (name N or name CA or name C or name O or name CB \ )) or resid 607 through 608 or (resid 609 and (name N or name CA or name C or na \ me O or name CB )) or resid 610 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 621 or (resid 622 and (n \ ame N or name CA or name C or name O or name CB )) or resid 623 through 626)) selection = (chain 'D' and (resid 22 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 55 or (resid 56 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throu \ gh 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 175 or (resid 176 through 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 180 or (resid 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 through 2 \ 85 or (resid 286 and (name N or name CA or name C or name O or name CB )) or res \ id 287 through 302 or (resid 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 304 through 332 or (resid 333 and (name N or name CA or name \ C or name O or name CB )) or resid 334 through 339 or (resid 340 and (name N or \ name CA or name C or name O or name CB )) or resid 341 through 370 or (resid 371 \ and (name N or name CA or name C or name O or name CB )) or resid 372 through 4 \ 05 or (resid 406 and (name N or name CA or name C or name O or name CB )) or res \ id 407 through 414 or (resid 415 through 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 through 429 or (resid 430 through 431 and (na \ me N or name CA or name C or name O or name CB )) or resid 432 through 436 or (r \ esid 437 and (name N or name CA or name C or name O or name CB )) or resid 438 t \ hrough 446 or (resid 447 through 448 and (name N or name CA or name C or name O \ or name CB )) or resid 449 through 480 or (resid 481 and (name N or name CA or n \ ame C or name O or name CB )) or resid 482 through 509 or (resid 510 and (name N \ or name CA or name C or name O or name CB )) or resid 511 through 605 or (resid \ 606 and (name N or name CA or name C or name O or name CB )) or resid 607 throu \ gh 608 or (resid 609 and (name N or name CA or name C or name O or name CB )) or \ resid 610 through 618 or (resid 619 and (name N or name CA or name C or name O \ or name CB )) or resid 620 through 621 or (resid 622 and (name N or name CA or n \ ame C or name O or name CB )) or resid 623 through 626)) } ncs_group { reference = (chain 'E' and resid 316 through 349) selection = (chain 'F' and resid 316 through 349) selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 232 or resid 238 through 262 or (resid 263 and ( \ name N or name CA or name C or name O or name CB )) or resid 264 through 266)) selection = (chain 'J' and (resid 1 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 266)) } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.680 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 66.690 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.008 0.057 25158 Z= 0.539 Angle : 1.574 15.081 34151 Z= 1.076 Chirality : 0.131 0.799 3720 Planarity : 0.009 0.054 4381 Dihedral : 14.871 89.453 8974 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 5.85 % Allowed : 10.69 % Favored : 83.46 % Cbeta Deviations : 1.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3040 helix: 0.86 (0.12), residues: 1504 sheet: -1.30 (0.27), residues: 383 loop : -1.04 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.009 TRP C 34 HIS 0.026 0.007 HIS B 297 PHE 0.073 0.009 PHE B 154 TYR 0.081 0.008 TYR C 572 ARG 0.024 0.003 ARG D 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 732 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 60 MET cc_start: 0.7787 (mmm) cc_final: 0.7535 (mmm) REVERT: J 95 TYR cc_start: 0.7608 (m-80) cc_final: 0.7125 (m-80) REVERT: J 113 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7669 (t0) REVERT: J 130 ASP cc_start: 0.8313 (m-30) cc_final: 0.7227 (m-30) REVERT: B 24 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.6008 (mt) REVERT: B 108 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.5770 (pp) REVERT: B 116 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.4247 (tp) REVERT: B 171 GLU cc_start: 0.2827 (OUTLIER) cc_final: 0.2441 (tp30) REVERT: B 292 GLU cc_start: 0.1888 (OUTLIER) cc_final: -0.0227 (tt0) REVERT: B 296 LEU cc_start: 0.5286 (mp) cc_final: 0.5045 (mt) REVERT: B 319 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8236 (m-40) REVERT: B 337 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6868 (ttmm) REVERT: B 361 THR cc_start: 0.8518 (m) cc_final: 0.8227 (p) REVERT: B 463 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 542 ILE cc_start: 0.3393 (tp) cc_final: 0.3004 (pt) REVERT: C 62 TYR cc_start: 0.8288 (t80) cc_final: 0.7397 (t80) REVERT: C 80 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7623 (mp) REVERT: C 106 TRP cc_start: 0.8547 (t60) cc_final: 0.8276 (t60) REVERT: C 229 VAL cc_start: 0.7842 (p) cc_final: 0.7402 (p) REVERT: C 372 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7380 (t) REVERT: C 448 MET cc_start: 0.8235 (mmm) cc_final: 0.7857 (mmt) REVERT: C 562 ASP cc_start: 0.8282 (m-30) cc_final: 0.7942 (t0) REVERT: C 579 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7627 (ttt-90) REVERT: C 603 ARG cc_start: 0.6989 (ttp80) cc_final: 0.6620 (tmt170) REVERT: D 68 TYR cc_start: 0.7543 (t80) cc_final: 0.7331 (t80) REVERT: D 100 LYS cc_start: 0.8266 (mttt) cc_final: 0.7769 (tptt) REVERT: D 138 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7201 (m110) REVERT: D 147 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7554 (mm-30) REVERT: D 259 SER cc_start: 0.8227 (t) cc_final: 0.7790 (p) REVERT: D 333 GLU cc_start: 0.7025 (tp30) cc_final: 0.6721 (tp30) REVERT: D 337 LYS cc_start: 0.8327 (mptp) cc_final: 0.8024 (tptt) REVERT: D 387 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8313 (tptt) REVERT: D 419 MET cc_start: 0.7604 (mmp) cc_final: 0.7336 (mmp) REVERT: D 480 GLU cc_start: 0.8261 (tt0) cc_final: 0.7962 (tp30) REVERT: D 491 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8259 (m) REVERT: D 579 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7427 (tpp80) REVERT: D 619 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7796 (pm20) REVERT: A 48 GLN cc_start: 0.8029 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 70 GLU cc_start: 0.8467 (tt0) cc_final: 0.8153 (mt-10) REVERT: A 109 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8009 (pm20) REVERT: A 135 ASP cc_start: 0.8431 (m-30) cc_final: 0.8044 (t70) REVERT: A 303 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8070 (tpt170) REVERT: A 319 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8368 (t0) REVERT: A 422 LYS cc_start: 0.7938 (pttt) cc_final: 0.7668 (tppt) REVERT: A 423 GLU cc_start: 0.8644 (pt0) cc_final: 0.8301 (tp30) REVERT: A 586 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6894 (tpp80) REVERT: A 600 TYR cc_start: 0.7686 (t80) cc_final: 0.7457 (t80) REVERT: E 316 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.5982 (t) REVERT: E 317 SER cc_start: 0.6859 (OUTLIER) cc_final: 0.6293 (p) REVERT: I 30 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7530 (mmt180) REVERT: I 156 GLN cc_start: 0.8574 (mt0) cc_final: 0.8271 (tm-30) REVERT: H 316 VAL cc_start: 0.2848 (OUTLIER) cc_final: 0.2581 (t) REVERT: H 333 MET cc_start: 0.8392 (mmm) cc_final: 0.8080 (pmm) outliers start: 152 outliers final: 46 residues processed: 829 average time/residue: 0.3944 time to fit residues: 492.8422 Evaluate side-chains 509 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 447 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 348 TYR Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 78 optimal weight: 0.0040 chunk 155 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 276 optimal weight: 7.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 GLN J 140 GLN J 164 GLN B 95 ASN B 138 ASN ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN B 541 HIS B 581 GLN B 587 ASN C 178 HIS C 222 ASN C 283 ASN C 295 ASN C 299 GLN C 388 GLN C 436 GLN C 467 ASN D 305 GLN D 315 HIS D 360 GLN D 383 GLN D 436 GLN D 576 GLN D 581 GLN D 587 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS A 260 GLN A 299 GLN A 388 GLN A 417 ASN A 446 HIS A 530 ASN A 577 GLN A 587 ASN E 350 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN I 164 GLN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25158 Z= 0.230 Angle : 0.629 9.424 34151 Z= 0.334 Chirality : 0.044 0.232 3720 Planarity : 0.004 0.058 4381 Dihedral : 7.450 71.145 3449 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 5.04 % Allowed : 15.65 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3040 helix: 1.58 (0.13), residues: 1529 sheet: -1.13 (0.26), residues: 390 loop : -0.64 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 34 HIS 0.008 0.001 HIS C 240 PHE 0.027 0.002 PHE C 156 TYR 0.026 0.002 TYR G 332 ARG 0.008 0.001 ARG D 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 472 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7614 (m-80) cc_final: 0.7104 (m-80) REVERT: J 113 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7696 (t0) REVERT: B 292 GLU cc_start: 0.2584 (OUTLIER) cc_final: 0.0675 (tt0) REVERT: B 337 LYS cc_start: 0.7301 (mmtp) cc_final: 0.7096 (mmtp) REVERT: B 361 THR cc_start: 0.8602 (m) cc_final: 0.8326 (p) REVERT: B 378 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7763 (mt-10) REVERT: B 548 TYR cc_start: 0.5439 (OUTLIER) cc_final: 0.5153 (t80) REVERT: B 600 TYR cc_start: 0.5128 (t80) cc_final: 0.4897 (t80) REVERT: C 24 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6316 (pp) REVERT: C 416 MET cc_start: 0.7570 (mmm) cc_final: 0.7126 (mmm) REVERT: C 448 MET cc_start: 0.8089 (mmm) cc_final: 0.7626 (mmt) REVERT: C 450 ASP cc_start: 0.6343 (t0) cc_final: 0.5994 (p0) REVERT: C 530 ASN cc_start: 0.7924 (t0) cc_final: 0.7665 (t0) REVERT: C 562 ASP cc_start: 0.8283 (m-30) cc_final: 0.7985 (t0) REVERT: D 100 LYS cc_start: 0.8199 (mttt) cc_final: 0.7705 (tptt) REVERT: D 147 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7557 (mm-30) REVERT: D 174 HIS cc_start: 0.6562 (m-70) cc_final: 0.6311 (m90) REVERT: D 315 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7905 (m90) REVERT: D 333 GLU cc_start: 0.6991 (tp30) cc_final: 0.6572 (tp30) REVERT: D 387 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8121 (tptt) REVERT: D 419 MET cc_start: 0.7326 (mmp) cc_final: 0.7110 (mmp) REVERT: D 437 ARG cc_start: 0.6095 (ttm170) cc_final: 0.5752 (ttp-170) REVERT: D 480 GLU cc_start: 0.8196 (tt0) cc_final: 0.7924 (mm-30) REVERT: D 611 MET cc_start: 0.7276 (mmm) cc_final: 0.7031 (mtt) REVERT: D 619 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7799 (pm20) REVERT: A 48 GLN cc_start: 0.7908 (tt0) cc_final: 0.7564 (tm-30) REVERT: A 100 LYS cc_start: 0.7182 (mtmp) cc_final: 0.6889 (mtmm) REVERT: A 102 TYR cc_start: 0.8101 (m-80) cc_final: 0.7765 (m-10) REVERT: A 109 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8080 (pm20) REVERT: A 135 ASP cc_start: 0.8273 (m-30) cc_final: 0.8024 (t0) REVERT: A 319 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 333 GLU cc_start: 0.7500 (tp30) cc_final: 0.7066 (mt-10) REVERT: A 422 LYS cc_start: 0.7480 (pttt) cc_final: 0.7180 (tppp) REVERT: A 423 GLU cc_start: 0.8578 (pt0) cc_final: 0.8191 (tp30) REVERT: I 30 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.7609 (mmt-90) REVERT: I 42 GLN cc_start: 0.7327 (tt0) cc_final: 0.6850 (tm-30) REVERT: I 156 GLN cc_start: 0.8670 (mt0) cc_final: 0.8022 (tm-30) REVERT: H 333 MET cc_start: 0.8536 (mmm) cc_final: 0.8147 (pmm) outliers start: 131 outliers final: 63 residues processed: 565 average time/residue: 0.3860 time to fit residues: 339.6165 Evaluate side-chains 464 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 395 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain J residue 241 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 315 HIS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 6.9990 chunk 85 optimal weight: 0.0040 chunk 229 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 276 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 GLN ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN C 222 ASN C 223 ASN D 223 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** I 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 182 HIS I 239 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25158 Z= 0.270 Angle : 0.598 12.967 34151 Z= 0.312 Chirality : 0.043 0.237 3720 Planarity : 0.004 0.074 4381 Dihedral : 6.303 74.731 3393 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.23 % Allowed : 17.69 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3040 helix: 1.47 (0.13), residues: 1528 sheet: -1.30 (0.25), residues: 397 loop : -0.53 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 34 HIS 0.018 0.001 HIS D 315 PHE 0.023 0.002 PHE C 63 TYR 0.032 0.002 TYR H 332 ARG 0.009 0.001 ARG G 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 418 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 80 LEU cc_start: 0.7153 (mt) cc_final: 0.6939 (mp) REVERT: J 95 TYR cc_start: 0.7712 (m-80) cc_final: 0.7120 (m-80) REVERT: J 113 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7710 (t0) REVERT: J 130 ASP cc_start: 0.8417 (m-30) cc_final: 0.7354 (m-30) REVERT: B 360 GLN cc_start: 0.7645 (mt0) cc_final: 0.7364 (mm-40) REVERT: B 378 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7795 (mt-10) REVERT: B 390 TRP cc_start: 0.8629 (t-100) cc_final: 0.8253 (t60) REVERT: B 542 ILE cc_start: 0.4453 (mm) cc_final: 0.3308 (pt) REVERT: B 548 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.5388 (t80) REVERT: B 600 TYR cc_start: 0.5065 (t80) cc_final: 0.4825 (t80) REVERT: C 448 MET cc_start: 0.7961 (mmm) cc_final: 0.7483 (mmt) REVERT: C 450 ASP cc_start: 0.6468 (t0) cc_final: 0.6060 (p0) REVERT: C 615 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8244 (ttmt) REVERT: D 135 ASP cc_start: 0.9070 (m-30) cc_final: 0.8797 (t0) REVERT: D 174 HIS cc_start: 0.6344 (m-70) cc_final: 0.6102 (m90) REVERT: D 315 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.8266 (m-70) REVERT: D 387 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8172 (tptt) REVERT: D 415 ASP cc_start: 0.7402 (t0) cc_final: 0.7172 (t0) REVERT: D 419 MET cc_start: 0.7200 (mmp) cc_final: 0.6909 (mmp) REVERT: D 480 GLU cc_start: 0.8250 (tt0) cc_final: 0.8006 (tp30) REVERT: D 539 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: D 619 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7853 (pm20) REVERT: A 100 LYS cc_start: 0.7304 (mtmp) cc_final: 0.7003 (mtmm) REVERT: A 102 TYR cc_start: 0.8166 (m-80) cc_final: 0.7751 (m-10) REVERT: A 109 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8010 (pm20) REVERT: A 135 ASP cc_start: 0.8170 (m-30) cc_final: 0.7901 (t0) REVERT: A 319 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (t0) REVERT: A 333 GLU cc_start: 0.7452 (tp30) cc_final: 0.6997 (mt-10) REVERT: A 422 LYS cc_start: 0.7523 (pttt) cc_final: 0.7260 (tppp) REVERT: A 423 GLU cc_start: 0.8460 (pt0) cc_final: 0.8026 (tp30) REVERT: E 333 MET cc_start: 0.9185 (mmm) cc_final: 0.8634 (mtt) REVERT: I 30 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.7618 (mmt-90) REVERT: I 42 GLN cc_start: 0.7599 (tt0) cc_final: 0.7045 (tm-30) REVERT: H 333 MET cc_start: 0.8473 (mmm) cc_final: 0.7907 (pmm) outliers start: 110 outliers final: 75 residues processed: 492 average time/residue: 0.3650 time to fit residues: 282.5970 Evaluate side-chains 452 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 372 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 315 HIS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 277 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN D 315 HIS ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN I 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25158 Z= 0.260 Angle : 0.574 13.518 34151 Z= 0.298 Chirality : 0.042 0.232 3720 Planarity : 0.004 0.060 4381 Dihedral : 5.742 53.130 3380 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.62 % Allowed : 18.31 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3040 helix: 1.47 (0.13), residues: 1531 sheet: -1.37 (0.25), residues: 396 loop : -0.47 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 34 HIS 0.008 0.001 HIS D 315 PHE 0.023 0.002 PHE C 63 TYR 0.030 0.002 TYR H 332 ARG 0.006 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 393 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 47 MET cc_start: 0.7399 (mmp) cc_final: 0.7149 (ttp) REVERT: J 95 TYR cc_start: 0.7690 (m-80) cc_final: 0.7038 (m-80) REVERT: J 113 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7662 (t0) REVERT: J 130 ASP cc_start: 0.8426 (m-30) cc_final: 0.7224 (m-30) REVERT: J 222 TYR cc_start: 0.7797 (m-80) cc_final: 0.7490 (m-80) REVERT: B 94 MET cc_start: 0.2723 (mmp) cc_final: 0.2513 (mmt) REVERT: B 244 MET cc_start: 0.3368 (mmt) cc_final: 0.3075 (tpp) REVERT: B 351 TYR cc_start: 0.7403 (t80) cc_final: 0.6466 (m-80) REVERT: B 378 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7760 (mt-10) REVERT: B 390 TRP cc_start: 0.8678 (t-100) cc_final: 0.8281 (t60) REVERT: B 494 GLU cc_start: 0.6512 (tt0) cc_final: 0.6191 (mp0) REVERT: B 542 ILE cc_start: 0.4371 (mm) cc_final: 0.3250 (pt) REVERT: B 548 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5432 (t80) REVERT: B 600 TYR cc_start: 0.5010 (t80) cc_final: 0.4711 (t80) REVERT: C 448 MET cc_start: 0.7820 (mmm) cc_final: 0.7465 (mmt) REVERT: C 450 ASP cc_start: 0.6528 (t0) cc_final: 0.6178 (p0) REVERT: C 615 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8256 (ttmt) REVERT: D 135 ASP cc_start: 0.9028 (m-30) cc_final: 0.8784 (t0) REVERT: D 387 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8192 (tptt) REVERT: D 480 GLU cc_start: 0.8262 (tt0) cc_final: 0.7891 (tp30) REVERT: D 619 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7898 (pm20) REVERT: A 100 LYS cc_start: 0.7188 (mtmp) cc_final: 0.6771 (mtmm) REVERT: A 102 TYR cc_start: 0.8130 (m-80) cc_final: 0.7618 (m-10) REVERT: A 135 ASP cc_start: 0.8215 (m-30) cc_final: 0.7955 (t0) REVERT: A 319 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.8291 (t0) REVERT: A 333 GLU cc_start: 0.7473 (tp30) cc_final: 0.7049 (mt-10) REVERT: A 422 LYS cc_start: 0.7508 (pttt) cc_final: 0.7180 (tppp) REVERT: A 423 GLU cc_start: 0.8448 (pt0) cc_final: 0.7956 (tp30) REVERT: E 333 MET cc_start: 0.9192 (mmm) cc_final: 0.8649 (mtt) REVERT: I 30 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.7682 (mmt180) REVERT: I 42 GLN cc_start: 0.7591 (tt0) cc_final: 0.6931 (tm-30) REVERT: H 333 MET cc_start: 0.8483 (mmm) cc_final: 0.7878 (pmm) outliers start: 120 outliers final: 80 residues processed: 480 average time/residue: 0.3448 time to fit residues: 260.7412 Evaluate side-chains 442 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 359 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 203 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 263 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 182 HIS ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 205 HIS B 280 ASN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN D 174 HIS D 383 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25158 Z= 0.233 Angle : 0.553 13.194 34151 Z= 0.287 Chirality : 0.041 0.219 3720 Planarity : 0.004 0.057 4381 Dihedral : 5.595 53.259 3379 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.54 % Allowed : 18.92 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3040 helix: 1.49 (0.13), residues: 1528 sheet: -1.43 (0.25), residues: 405 loop : -0.54 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 174 HIS 0.008 0.001 HIS J 182 PHE 0.029 0.002 PHE D 312 TYR 0.031 0.002 TYR H 332 ARG 0.005 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 395 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 47 MET cc_start: 0.7473 (mmp) cc_final: 0.7180 (ttp) REVERT: J 95 TYR cc_start: 0.7625 (m-80) cc_final: 0.6984 (m-80) REVERT: J 113 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7657 (t0) REVERT: J 130 ASP cc_start: 0.8498 (m-30) cc_final: 0.7291 (m-30) REVERT: B 351 TYR cc_start: 0.7471 (t80) cc_final: 0.6640 (m-80) REVERT: B 378 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7755 (mt-10) REVERT: B 390 TRP cc_start: 0.8687 (t-100) cc_final: 0.8243 (t60) REVERT: B 494 GLU cc_start: 0.6542 (tt0) cc_final: 0.6203 (mp0) REVERT: B 542 ILE cc_start: 0.4571 (mm) cc_final: 0.3462 (pt) REVERT: B 548 TYR cc_start: 0.5677 (OUTLIER) cc_final: 0.5466 (t80) REVERT: B 600 TYR cc_start: 0.5007 (t80) cc_final: 0.4579 (t80) REVERT: C 204 THR cc_start: 0.9118 (p) cc_final: 0.8852 (t) REVERT: C 419 MET cc_start: 0.6929 (mmt) cc_final: 0.6634 (mmt) REVERT: C 615 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8240 (ttmt) REVERT: D 135 ASP cc_start: 0.8976 (m-30) cc_final: 0.8741 (t0) REVERT: D 180 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (m170) REVERT: D 387 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8171 (tptt) REVERT: D 480 GLU cc_start: 0.8286 (tt0) cc_final: 0.7927 (tp30) REVERT: D 592 LEU cc_start: 0.8748 (tp) cc_final: 0.8500 (tp) REVERT: D 619 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7776 (pm20) REVERT: A 100 LYS cc_start: 0.6997 (mtmp) cc_final: 0.6645 (mtmm) REVERT: A 102 TYR cc_start: 0.8082 (m-80) cc_final: 0.7605 (m-10) REVERT: A 135 ASP cc_start: 0.8236 (m-30) cc_final: 0.8000 (t0) REVERT: A 319 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8304 (t0) REVERT: A 333 GLU cc_start: 0.7481 (tp30) cc_final: 0.7053 (mt-10) REVERT: E 333 MET cc_start: 0.9170 (mmm) cc_final: 0.8638 (mtt) REVERT: I 30 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.7731 (mmt180) REVERT: I 42 GLN cc_start: 0.7630 (tt0) cc_final: 0.6966 (tm-30) REVERT: H 333 MET cc_start: 0.8459 (mmm) cc_final: 0.7820 (pmm) outliers start: 118 outliers final: 86 residues processed: 478 average time/residue: 0.3574 time to fit residues: 269.9452 Evaluate side-chains 449 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 359 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 378 GLU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 294 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 205 HIS B 280 ASN C 149 ASN D 174 HIS D 315 HIS D 587 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25158 Z= 0.192 Angle : 0.535 13.376 34151 Z= 0.276 Chirality : 0.040 0.215 3720 Planarity : 0.004 0.057 4381 Dihedral : 5.369 53.720 3375 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.81 % Allowed : 20.19 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.15), residues: 3040 helix: 1.56 (0.13), residues: 1527 sheet: -1.40 (0.26), residues: 406 loop : -0.51 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 34 HIS 0.018 0.001 HIS B 178 PHE 0.021 0.001 PHE A 481 TYR 0.027 0.001 TYR A 509 ARG 0.012 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 372 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 47 MET cc_start: 0.7515 (mmp) cc_final: 0.7247 (ttp) REVERT: J 95 TYR cc_start: 0.7642 (m-80) cc_final: 0.6978 (m-80) REVERT: J 113 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7690 (t0) REVERT: B 94 MET cc_start: 0.3048 (mmp) cc_final: 0.1535 (mmm) REVERT: B 166 LEU cc_start: 0.2055 (OUTLIER) cc_final: 0.1572 (pp) REVERT: B 351 TYR cc_start: 0.7497 (t80) cc_final: 0.6654 (m-80) REVERT: B 378 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7712 (mt-10) REVERT: B 390 TRP cc_start: 0.8701 (t-100) cc_final: 0.8262 (t60) REVERT: B 494 GLU cc_start: 0.6608 (tt0) cc_final: 0.6307 (mp0) REVERT: B 542 ILE cc_start: 0.4400 (mm) cc_final: 0.3335 (pt) REVERT: B 567 LEU cc_start: 0.7700 (tp) cc_final: 0.6629 (tt) REVERT: B 600 TYR cc_start: 0.5038 (t80) cc_final: 0.4610 (t80) REVERT: C 419 MET cc_start: 0.6952 (mmt) cc_final: 0.6664 (mmt) REVERT: C 615 LYS cc_start: 0.8591 (mmtm) cc_final: 0.8236 (ttmt) REVERT: D 100 LYS cc_start: 0.8175 (mttt) cc_final: 0.7695 (tptt) REVERT: D 135 ASP cc_start: 0.8948 (m-30) cc_final: 0.8711 (t0) REVERT: D 221 TYR cc_start: 0.6976 (m-80) cc_final: 0.6271 (m-80) REVERT: D 387 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8139 (tptt) REVERT: D 480 GLU cc_start: 0.8284 (tt0) cc_final: 0.7911 (tp30) REVERT: D 592 LEU cc_start: 0.8717 (tp) cc_final: 0.8478 (tp) REVERT: D 619 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7792 (pm20) REVERT: A 135 ASP cc_start: 0.8201 (m-30) cc_final: 0.7965 (t0) REVERT: A 319 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 333 GLU cc_start: 0.7382 (tp30) cc_final: 0.6982 (mt-10) REVERT: E 333 MET cc_start: 0.9199 (mmm) cc_final: 0.8677 (mtt) REVERT: I 30 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.7730 (mmt180) REVERT: I 42 GLN cc_start: 0.7611 (tt0) cc_final: 0.6965 (tm-30) outliers start: 99 outliers final: 73 residues processed: 446 average time/residue: 0.3526 time to fit residues: 250.1023 Evaluate side-chains 428 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 352 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 2.9990 chunk 33 optimal weight: 30.0000 chunk 167 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 135 optimal weight: 0.2980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 242 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN C 149 ASN D 174 HIS D 577 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25158 Z= 0.327 Angle : 0.598 14.345 34151 Z= 0.309 Chirality : 0.043 0.244 3720 Planarity : 0.004 0.062 4381 Dihedral : 5.511 56.886 3374 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.31 % Allowed : 19.77 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3040 helix: 1.35 (0.13), residues: 1532 sheet: -1.57 (0.26), residues: 383 loop : -0.69 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 34 HIS 0.007 0.001 HIS C 478 PHE 0.029 0.002 PHE D 312 TYR 0.044 0.002 TYR B 548 ARG 0.016 0.001 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 381 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 47 MET cc_start: 0.7537 (mmp) cc_final: 0.7279 (ttp) REVERT: J 95 TYR cc_start: 0.7647 (m-80) cc_final: 0.6898 (m-80) REVERT: J 113 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7728 (t0) REVERT: J 115 PHE cc_start: 0.6613 (m-10) cc_final: 0.6235 (m-10) REVERT: J 130 ASP cc_start: 0.8711 (m-30) cc_final: 0.7487 (m-30) REVERT: J 160 ASP cc_start: 0.7699 (t0) cc_final: 0.7453 (m-30) REVERT: B 94 MET cc_start: 0.3028 (mmp) cc_final: 0.1915 (mmt) REVERT: B 250 HIS cc_start: 0.6592 (t70) cc_final: 0.6163 (p-80) REVERT: B 251 CYS cc_start: 0.7222 (m) cc_final: 0.6517 (p) REVERT: B 378 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7684 (mt-10) REVERT: B 448 MET cc_start: 0.8135 (mtp) cc_final: 0.7884 (mtm) REVERT: B 494 GLU cc_start: 0.6768 (tt0) cc_final: 0.6454 (mp0) REVERT: B 542 ILE cc_start: 0.4430 (mm) cc_final: 0.3297 (pt) REVERT: C 419 MET cc_start: 0.7011 (mmt) cc_final: 0.6787 (mmt) REVERT: C 448 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6238 (mmt) REVERT: C 595 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7739 (tt) REVERT: C 615 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8310 (ttmt) REVERT: D 100 LYS cc_start: 0.8152 (mttt) cc_final: 0.7713 (tptt) REVERT: D 135 ASP cc_start: 0.8954 (m-30) cc_final: 0.8717 (t0) REVERT: D 219 ASP cc_start: 0.6975 (t0) cc_final: 0.6454 (t70) REVERT: D 336 ASN cc_start: 0.8742 (m-40) cc_final: 0.8534 (m-40) REVERT: D 387 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8206 (tptt) REVERT: D 480 GLU cc_start: 0.8339 (tt0) cc_final: 0.8039 (tp30) REVERT: D 592 LEU cc_start: 0.8810 (tp) cc_final: 0.8599 (tp) REVERT: D 619 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7970 (pm20) REVERT: A 100 LYS cc_start: 0.6697 (mtmm) cc_final: 0.6394 (mttp) REVERT: A 102 TYR cc_start: 0.8143 (m-80) cc_final: 0.7837 (m-10) REVERT: A 135 ASP cc_start: 0.8204 (m-30) cc_final: 0.7938 (t0) REVERT: A 319 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8371 (t0) REVERT: E 333 MET cc_start: 0.9182 (mmm) cc_final: 0.8680 (mtt) REVERT: I 30 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.7774 (mmt180) REVERT: I 42 GLN cc_start: 0.7607 (tt0) cc_final: 0.7039 (tm-30) REVERT: I 130 ASP cc_start: 0.7022 (m-30) cc_final: 0.6810 (m-30) outliers start: 112 outliers final: 94 residues processed: 465 average time/residue: 0.3501 time to fit residues: 258.9662 Evaluate side-chains 450 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 352 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 448 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 230 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS D 174 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25158 Z= 0.224 Angle : 0.558 13.247 34151 Z= 0.287 Chirality : 0.042 0.327 3720 Planarity : 0.004 0.066 4381 Dihedral : 5.424 57.757 3374 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.96 % Allowed : 20.50 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3040 helix: 1.46 (0.13), residues: 1529 sheet: -1.51 (0.26), residues: 397 loop : -0.59 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 143 HIS 0.005 0.001 HIS C 240 PHE 0.021 0.002 PHE C 63 TYR 0.036 0.002 TYR B 548 ARG 0.017 0.000 ARG G 343 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 359 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 47 MET cc_start: 0.7639 (mmp) cc_final: 0.7266 (ttp) REVERT: J 95 TYR cc_start: 0.7660 (m-80) cc_final: 0.6967 (m-80) REVERT: J 113 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7765 (t0) REVERT: B 94 MET cc_start: 0.2875 (mmp) cc_final: 0.1919 (mmt) REVERT: B 244 MET cc_start: 0.3590 (mmm) cc_final: 0.3355 (tpp) REVERT: B 351 TYR cc_start: 0.7485 (t80) cc_final: 0.6662 (m-80) REVERT: B 378 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7713 (mt-10) REVERT: B 494 GLU cc_start: 0.6864 (tt0) cc_final: 0.6537 (mp0) REVERT: B 542 ILE cc_start: 0.4317 (mm) cc_final: 0.3214 (pt) REVERT: C 132 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: C 419 MET cc_start: 0.6959 (mmt) cc_final: 0.6743 (mmt) REVERT: C 615 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8262 (ttmt) REVERT: D 100 LYS cc_start: 0.8127 (mttt) cc_final: 0.7671 (tptt) REVERT: D 135 ASP cc_start: 0.8924 (m-30) cc_final: 0.8676 (t0) REVERT: D 219 ASP cc_start: 0.6942 (t0) cc_final: 0.6416 (t70) REVERT: D 378 GLU cc_start: 0.8157 (tt0) cc_final: 0.7939 (tp30) REVERT: D 387 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8174 (tptt) REVERT: D 480 GLU cc_start: 0.8367 (tt0) cc_final: 0.8020 (tp30) REVERT: D 592 LEU cc_start: 0.8790 (tp) cc_final: 0.8586 (tp) REVERT: D 619 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7920 (pm20) REVERT: A 100 LYS cc_start: 0.6487 (mtmm) cc_final: 0.6144 (mtmm) REVERT: A 102 TYR cc_start: 0.8156 (m-80) cc_final: 0.7846 (m-10) REVERT: A 135 ASP cc_start: 0.8244 (m-30) cc_final: 0.7896 (t0) REVERT: E 333 MET cc_start: 0.9189 (mmm) cc_final: 0.8691 (mtt) REVERT: I 30 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.7777 (mmt180) REVERT: I 42 GLN cc_start: 0.7559 (tt0) cc_final: 0.7004 (tm-30) REVERT: I 130 ASP cc_start: 0.6916 (m-30) cc_final: 0.6715 (m-30) outliers start: 103 outliers final: 90 residues processed: 439 average time/residue: 0.3727 time to fit residues: 260.1269 Evaluate side-chains 434 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 342 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.9990 chunk 280 optimal weight: 0.5980 chunk 256 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS D 223 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25158 Z= 0.202 Angle : 0.554 12.842 34151 Z= 0.285 Chirality : 0.042 0.348 3720 Planarity : 0.004 0.100 4381 Dihedral : 5.290 57.328 3372 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.65 % Allowed : 20.96 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3040 helix: 1.50 (0.13), residues: 1530 sheet: -1.42 (0.26), residues: 387 loop : -0.58 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 174 HIS 0.005 0.001 HIS B 240 PHE 0.023 0.001 PHE A 481 TYR 0.046 0.002 TYR B 548 ARG 0.016 0.000 ARG J 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 364 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7554 (m-80) cc_final: 0.6909 (m-80) REVERT: J 113 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7642 (t0) REVERT: J 115 PHE cc_start: 0.6934 (m-10) cc_final: 0.6493 (m-10) REVERT: B 221 TYR cc_start: 0.5261 (m-80) cc_final: 0.4729 (m-80) REVERT: B 244 MET cc_start: 0.3750 (mmm) cc_final: 0.3511 (tpp) REVERT: B 282 LEU cc_start: 0.8026 (mt) cc_final: 0.7752 (pt) REVERT: B 351 TYR cc_start: 0.7495 (t80) cc_final: 0.6673 (m-80) REVERT: B 378 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7777 (mt-10) REVERT: B 494 GLU cc_start: 0.6858 (tt0) cc_final: 0.6555 (mp0) REVERT: B 542 ILE cc_start: 0.4243 (mm) cc_final: 0.3069 (pt) REVERT: B 592 LEU cc_start: 0.7311 (mt) cc_final: 0.7052 (mt) REVERT: B 600 TYR cc_start: 0.5199 (t80) cc_final: 0.4739 (t80) REVERT: C 132 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: C 227 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: C 419 MET cc_start: 0.7044 (mmt) cc_final: 0.6833 (mmt) REVERT: C 615 LYS cc_start: 0.8551 (mmtm) cc_final: 0.8255 (ttmt) REVERT: D 100 LYS cc_start: 0.8144 (mttt) cc_final: 0.7689 (tptt) REVERT: D 135 ASP cc_start: 0.8908 (m-30) cc_final: 0.8675 (t0) REVERT: D 219 ASP cc_start: 0.6908 (t0) cc_final: 0.6479 (t70) REVERT: D 221 TYR cc_start: 0.7077 (m-80) cc_final: 0.6401 (m-80) REVERT: D 387 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8192 (tptt) REVERT: D 410 VAL cc_start: 0.8385 (t) cc_final: 0.8162 (m) REVERT: D 415 ASP cc_start: 0.7040 (t0) cc_final: 0.6409 (t0) REVERT: D 419 MET cc_start: 0.6843 (tpp) cc_final: 0.6106 (mpp) REVERT: D 480 GLU cc_start: 0.8376 (tt0) cc_final: 0.8041 (tp30) REVERT: D 619 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7913 (pm20) REVERT: A 100 LYS cc_start: 0.6590 (mtmm) cc_final: 0.6273 (mtmm) REVERT: A 102 TYR cc_start: 0.8141 (m-80) cc_final: 0.7891 (m-10) REVERT: A 135 ASP cc_start: 0.8229 (m-30) cc_final: 0.7886 (t0) REVERT: E 333 MET cc_start: 0.9197 (mmm) cc_final: 0.8691 (mtt) REVERT: I 30 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.7756 (mmt180) REVERT: I 42 GLN cc_start: 0.7537 (tt0) cc_final: 0.6975 (tm-30) outliers start: 95 outliers final: 80 residues processed: 442 average time/residue: 0.3466 time to fit residues: 242.2976 Evaluate side-chains 433 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 350 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 69 SER Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 302 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 25 optimal weight: 0.0570 chunk 186 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS B 299 GLN B 305 GLN D 174 HIS ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25158 Z= 0.183 Angle : 0.564 14.398 34151 Z= 0.286 Chirality : 0.041 0.368 3720 Planarity : 0.004 0.075 4381 Dihedral : 5.135 56.848 3371 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.81 % Allowed : 22.19 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 3040 helix: 1.56 (0.13), residues: 1524 sheet: -1.34 (0.26), residues: 393 loop : -0.54 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 174 HIS 0.005 0.001 HIS C 240 PHE 0.021 0.001 PHE B 537 TYR 0.039 0.001 TYR B 548 ARG 0.009 0.000 ARG C 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 365 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7525 (m-80) cc_final: 0.6911 (m-80) REVERT: J 104 ASP cc_start: 0.7352 (p0) cc_final: 0.6272 (t0) REVERT: J 113 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7678 (t0) REVERT: J 130 ASP cc_start: 0.8532 (m-30) cc_final: 0.8117 (t0) REVERT: B 94 MET cc_start: 0.3009 (mmp) cc_final: 0.1879 (mmt) REVERT: B 221 TYR cc_start: 0.5149 (m-80) cc_final: 0.4858 (m-80) REVERT: B 244 MET cc_start: 0.3577 (mmm) cc_final: 0.3269 (tpp) REVERT: B 282 LEU cc_start: 0.7962 (mt) cc_final: 0.7696 (pt) REVERT: B 351 TYR cc_start: 0.7502 (t80) cc_final: 0.6670 (m-80) REVERT: B 378 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7747 (mt-10) REVERT: B 494 GLU cc_start: 0.6830 (tt0) cc_final: 0.6544 (mp0) REVERT: B 542 ILE cc_start: 0.4074 (mm) cc_final: 0.2970 (pt) REVERT: C 227 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.6769 (m-80) REVERT: C 419 MET cc_start: 0.6996 (mmt) cc_final: 0.6789 (mmt) REVERT: C 615 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8156 (ttmt) REVERT: D 100 LYS cc_start: 0.8143 (mttt) cc_final: 0.7680 (tptt) REVERT: D 135 ASP cc_start: 0.8925 (m-30) cc_final: 0.8672 (t0) REVERT: D 145 ASP cc_start: 0.8473 (t0) cc_final: 0.8168 (t0) REVERT: D 219 ASP cc_start: 0.6904 (t0) cc_final: 0.6371 (t70) REVERT: D 387 LYS cc_start: 0.8408 (ttmm) cc_final: 0.8123 (tptt) REVERT: D 410 VAL cc_start: 0.8313 (t) cc_final: 0.8105 (m) REVERT: D 480 GLU cc_start: 0.8377 (tt0) cc_final: 0.8029 (tp30) REVERT: D 619 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7838 (pm20) REVERT: A 78 GLU cc_start: 0.7478 (tt0) cc_final: 0.6790 (pm20) REVERT: A 100 LYS cc_start: 0.6538 (mtmm) cc_final: 0.6210 (mtmm) REVERT: A 102 TYR cc_start: 0.8127 (m-80) cc_final: 0.7866 (m-10) REVERT: A 135 ASP cc_start: 0.8222 (m-30) cc_final: 0.7873 (t0) REVERT: A 160 TRP cc_start: 0.6465 (t60) cc_final: 0.6231 (t60) REVERT: E 333 MET cc_start: 0.9182 (mmm) cc_final: 0.8668 (mtt) REVERT: I 30 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.7729 (mmt180) REVERT: I 42 GLN cc_start: 0.7501 (tt0) cc_final: 0.6956 (tm-30) outliers start: 73 outliers final: 63 residues processed: 423 average time/residue: 0.3640 time to fit residues: 239.7576 Evaluate side-chains 410 residues out of total 2665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 345 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 222 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS D 174 HIS ** A 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.195626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153411 restraints weight = 30983.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152871 restraints weight = 23182.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.153919 restraints weight = 27030.538| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25158 Z= 0.256 Angle : 0.595 15.417 34151 Z= 0.303 Chirality : 0.043 0.352 3720 Planarity : 0.005 0.114 4381 Dihedral : 5.124 56.948 3369 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.77 % Allowed : 22.12 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3040 helix: 1.48 (0.13), residues: 1526 sheet: -1.39 (0.27), residues: 383 loop : -0.58 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 134 HIS 0.020 0.001 HIS B 250 PHE 0.025 0.002 PHE J 245 TYR 0.058 0.002 TYR H 332 ARG 0.018 0.001 ARG G 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5689.37 seconds wall clock time: 104 minutes 5.52 seconds (6245.52 seconds total)