Starting phenix.real_space_refine on Sun Mar 17 08:47:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agb_15419/03_2024/8agb_15419_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.061 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 11307 2.51 5 N 2669 2.21 5 O 3163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 649": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E GLU 385": "OE1" <-> "OE2" Residue "E GLU 388": "OE1" <-> "OE2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F ARG 281": "NH1" <-> "NH2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H ARG 295": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17202 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5165 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 618} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 258 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "D" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 899 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "E" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3499 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 2 Chain: "F" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1914 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 15, 'TRANS': 239} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3201 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 973 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain breaks: 1 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'GLC': 3, 'MAN': 5, 'NAG': 1, 'NDG': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 124 Unusual residues: {' MG': 1, 'CPL': 1, 'ELU': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'CPL': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.62, per 1000 atoms: 0.56 Number of scatterers: 17202 At special positions: 0 Unit cell: (124.1, 113.9, 153.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 8 15.00 Mg 1 11.99 O 3163 8.00 N 2669 7.00 C 11307 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=1, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " " MAN I 5 " - " MAN I 6 " " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " GLC L 8 " - " GLC L 9 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA L 3 " - " MAN L 4 " " MAN L 6 " - " GLC L 7 " " GLC L 7 " - " GLC L 8 " " MAN L 10 " - " MAN L 11 " ALPHA1-6 " BMA I 3 " - " MAN I 7 " " BMA L 3 " - " MAN L 10 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NDG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG G 502 " - " ASN G 332 " " NAG G 503 " - " ASN G 60 " " NAG I 1 " - " ASN A 539 " " NAG J 1 " - " ASN E 336 " " NAG K 1 " - " ASN E 400 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 3.0 seconds 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3934 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 19 sheets defined 41.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.970A pdb=" N THR A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 25 " --> pdb=" O PHE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 removed outlier: 3.689A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 118 through 137 removed outlier: 3.969A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 4.037A pdb=" N ILE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 160 removed outlier: 4.824A pdb=" N ARG A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 188 removed outlier: 4.201A pdb=" N THR A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 209 through 227 removed outlier: 4.308A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 215 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.746A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 267 through 288 removed outlier: 3.544A pdb=" N GLN A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.694A pdb=" N PHE A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 Proline residue: A 371 - end of helix removed outlier: 3.812A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.765A pdb=" N PHE A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 Proline residue: A 411 - end of helix removed outlier: 3.570A pdb=" N ILE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 472 removed outlier: 3.572A pdb=" N VAL A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 540 through 550 removed outlier: 3.931A pdb=" N MET A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 564 removed outlier: 3.630A pdb=" N HIS A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 622 through 626 Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'B' and resid 4 through 31 Processing helix chain 'C' and resid 3 through 9 Processing helix chain 'C' and resid 22 through 46 Proline residue: C 26 - end of helix removed outlier: 4.532A pdb=" N VAL C 39 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 40 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 81 removed outlier: 3.612A pdb=" N ILE C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 66 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 40 Processing helix chain 'D' and resid 42 through 68 Processing helix chain 'D' and resid 74 through 99 Processing helix chain 'D' and resid 107 through 128 removed outlier: 3.603A pdb=" N PHE D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 270 through 279 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 443 through 446 No H-bonds generated for 'chain 'E' and resid 443 through 446' Processing helix chain 'E' and resid 448 through 468 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 194 through 217 removed outlier: 3.980A pdb=" N ILE F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE F 200 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 254 removed outlier: 4.328A pdb=" N LEU F 236 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F 243 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 282 Proline residue: F 271 - end of helix removed outlier: 4.058A pdb=" N LEU F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 49 removed outlier: 3.747A pdb=" N SER G 41 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL G 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR G 43 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS G 45 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 Processing helix chain 'G' and resid 96 through 104 Processing helix chain 'G' and resid 120 through 129 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'G' and resid 243 through 258 removed outlier: 5.532A pdb=" N GLU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE G 249 " --> pdb=" O SER G 245 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS G 251 " --> pdb=" O GLN G 247 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU G 252 " --> pdb=" O GLU G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 393 through 415 removed outlier: 3.605A pdb=" N VAL G 411 " --> pdb=" O ILE G 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 232 Processing helix chain 'H' and resid 236 through 240 Processing helix chain 'H' and resid 267 through 288 removed outlier: 3.626A pdb=" N VAL H 272 " --> pdb=" O GLU H 269 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET H 273 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL H 274 " --> pdb=" O GLN H 271 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA H 281 " --> pdb=" O GLY H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 298 removed outlier: 3.541A pdb=" N ARG H 295 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 334 Processing sheet with id= A, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.390A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 197 through 199 removed outlier: 3.841A pdb=" N GLU E 204 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 80 " --> pdb=" O PHE E 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 65 through 70 removed outlier: 3.758A pdb=" N ASN E 93 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 154 through 161 removed outlier: 3.728A pdb=" N GLN E 154 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 400 through 406 removed outlier: 3.977A pdb=" N ASN E 400 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 291 through 294 Processing sheet with id= G, first strand: chain 'E' and resid 349 through 351 removed outlier: 5.980A pdb=" N ASP E 440 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE E 389 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 231 through 236 removed outlier: 6.906A pdb=" N GLU E 256 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 32 through 34 removed outlier: 3.537A pdb=" N ASN F 70 " --> pdb=" O THR F 33 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 95 through 98 removed outlier: 6.671A pdb=" N LEU F 138 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU F 154 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU F 140 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N PHE F 152 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 26 through 28 Processing sheet with id= L, first strand: chain 'G' and resid 78 through 81 removed outlier: 6.650A pdb=" N ASN G 108 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL G 81 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU G 110 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 131 through 133 Processing sheet with id= N, first strand: chain 'G' and resid 139 through 142 removed outlier: 3.746A pdb=" N VAL G 139 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 151 through 154 Processing sheet with id= P, first strand: chain 'G' and resid 263 through 267 removed outlier: 3.731A pdb=" N VAL G 263 " --> pdb=" O TRP G 299 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 270 through 273 Processing sheet with id= R, first strand: chain 'G' and resid 297 through 299 Processing sheet with id= S, first strand: chain 'G' and resid 366 through 375 removed outlier: 4.012A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 1935 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: 5.13 Time building geometry restraints manager: 7.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2624 1.31 - 1.43: 5051 1.43 - 1.56: 9812 1.56 - 1.68: 65 1.68 - 1.81: 91 Bond restraints: 17643 Sorted by residual: bond pdb=" C31 CPL B 101 " pdb=" O2 CPL B 101 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C11 CPL B 101 " pdb=" O3 CPL B 101 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C31 CPL G 501 " pdb=" O2 CPL G 501 " ideal model delta sigma weight residual 1.332 1.431 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C31 CPL A 801 " pdb=" O2 CPL A 801 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 CPL A 801 " pdb=" O3 CPL A 801 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 17638 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.92: 365 105.92 - 113.00: 9609 113.00 - 120.09: 6291 120.09 - 127.17: 7461 127.17 - 134.25: 192 Bond angle restraints: 23918 Sorted by residual: angle pdb=" C14 ELU A 804 " pdb=" C13 ELU A 804 " pdb=" C15 ELU A 804 " ideal model delta sigma weight residual 68.19 119.66 -51.47 3.00e+00 1.11e-01 2.94e+02 angle pdb=" C12 ELU A 804 " pdb=" C13 ELU A 804 " pdb=" C15 ELU A 804 " ideal model delta sigma weight residual 85.86 121.50 -35.64 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C12 ELU A 804 " pdb=" C13 ELU A 804 " pdb=" C14 ELU A 804 " ideal model delta sigma weight residual 152.70 118.84 33.86 3.00e+00 1.11e-01 1.27e+02 angle pdb=" O3P CPL G 501 " pdb=" P CPL G 501 " pdb=" O4P CPL G 501 " ideal model delta sigma weight residual 93.29 110.74 -17.45 3.00e+00 1.11e-01 3.38e+01 angle pdb=" N ARG F 38 " pdb=" CA ARG F 38 " pdb=" C ARG F 38 " ideal model delta sigma weight residual 110.80 98.84 11.96 2.13e+00 2.20e-01 3.15e+01 ... (remaining 23913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 10114 33.44 - 66.88: 456 66.88 - 100.33: 50 100.33 - 133.77: 53 133.77 - 167.21: 5 Dihedral angle restraints: 10678 sinusoidal: 4590 harmonic: 6088 Sorted by residual: dihedral pdb=" CA TRP A 75 " pdb=" C TRP A 75 " pdb=" N TYR A 76 " pdb=" CA TYR A 76 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA SER F 37 " pdb=" C SER F 37 " pdb=" N ARG F 38 " pdb=" CA ARG F 38 " ideal model delta harmonic sigma weight residual 180.00 156.85 23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" O2 CPL E 501 " pdb=" C1 CPL E 501 " pdb=" C2 CPL E 501 " pdb=" O3P CPL E 501 " ideal model delta sinusoidal sigma weight residual -50.82 116.39 -167.21 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 10675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2276 0.061 - 0.123: 389 0.123 - 0.184: 53 0.184 - 0.246: 8 0.246 - 0.307: 7 Chirality restraints: 2733 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN E 400 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 539 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 2730 not shown) Planarity restraints: 2934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 CPL E 501 " -0.105 2.00e-02 2.50e+03 2.35e-01 5.54e+02 pdb=" C42 CPL E 501 " 0.319 2.00e-02 2.50e+03 pdb=" C43 CPL E 501 " -0.314 2.00e-02 2.50e+03 pdb=" C44 CPL E 501 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 CPL E 501 " 0.163 2.00e-02 2.50e+03 1.66e-01 2.75e+02 pdb=" C39 CPL E 501 " -0.155 2.00e-02 2.50e+03 pdb=" C40 CPL E 501 " -0.176 2.00e-02 2.50e+03 pdb=" C41 CPL E 501 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 56 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C LYS C 56 " -0.070 2.00e-02 2.50e+03 pdb=" O LYS C 56 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU C 57 " 0.024 2.00e-02 2.50e+03 ... (remaining 2931 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 175 2.62 - 3.19: 15234 3.19 - 3.76: 24872 3.76 - 4.33: 36945 4.33 - 4.90: 61414 Nonbonded interactions: 138640 Sorted by model distance: nonbonded pdb=" OD2 ASP A 166 " pdb="MG MG A 803 " model vdw 2.052 2.170 nonbonded pdb=" OH TYR F 253 " pdb=" OG SER G 386 " model vdw 2.209 2.440 nonbonded pdb="MG MG A 803 " pdb=" O1B ELU A 804 " model vdw 2.209 2.170 nonbonded pdb=" OE1 GLU E 252 " pdb=" OH TYR E 303 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASP A 110 " pdb=" N ILE A 111 " model vdw 2.272 2.520 ... (remaining 138635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.570 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 46.920 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.006 0.102 17643 Z= 0.389 Angle : 1.010 51.465 23918 Z= 0.462 Chirality : 0.050 0.307 2733 Planarity : 0.008 0.235 2929 Dihedral : 20.534 167.212 6744 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.28 % Rotamer: Outliers : 6.03 % Allowed : 20.88 % Favored : 73.09 % 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: -3.13 (0.16), residues: 2045 helix: -1.40 (0.16), residues: 841 sheet: -1.70 (0.25), residues: 385 loop : -2.89 (0.18), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 368 HIS 0.004 0.001 HIS E 286 PHE 0.029 0.001 PHE C 45 TYR 0.012 0.001 TYR A 501 ARG 0.004 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 184 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7933 (mtm110) REVERT: A 365 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8404 (t80) REVERT: A 691 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.9013 (p) REVERT: A 716 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8351 (mp) REVERT: D 69 ARG cc_start: 0.7567 (mmm160) cc_final: 0.6894 (tpp-160) REVERT: E 123 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6633 (pp) REVERT: E 204 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: E 205 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6896 (p90) REVERT: E 252 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: F 84 LEU cc_start: 0.8404 (tp) cc_final: 0.8171 (tt) REVERT: F 118 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8321 (tmmm) REVERT: F 134 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7021 (mp) REVERT: F 175 PHE cc_start: 0.5137 (OUTLIER) cc_final: 0.4302 (m-80) REVERT: G 236 ASP cc_start: 0.7864 (t0) cc_final: 0.7316 (t0) REVERT: H 239 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8220 (mp10) REVERT: H 271 GLN cc_start: 0.8360 (mt0) cc_final: 0.8145 (mt0) REVERT: H 291 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8401 (tp) outliers start: 108 outliers final: 35 residues processed: 280 average time/residue: 1.1550 time to fit residues: 364.5679 Evaluate side-chains 186 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 44 ASN Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 415 THR Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 2.9990 chunk 155 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 266 HIS A 277 GLN A 506 ASN A 653 GLN A 688 GLN B 6 GLN B 26 HIS C 21 HIS C 25 GLN C 80 ASN D 61 GLN D 122 HIS D 127 HIS E 93 ASN E 217 ASN E 226 HIS E 367 ASN E 416 HIS E 425 ASN F 90 ASN F 104 ASN F 159 ASN F 166 HIS F 217 ASN F 224 ASN G 157 HIS G 214 GLN G 226 ASN G 242 ASN G 243 GLN G 246 ASN G 271 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17643 Z= 0.163 Angle : 0.606 21.407 23918 Z= 0.291 Chirality : 0.044 0.279 2733 Planarity : 0.004 0.041 2929 Dihedral : 17.998 167.129 3049 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 4.58 % Allowed : 21.94 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.18), residues: 2045 helix: 0.32 (0.18), residues: 854 sheet: -0.91 (0.27), residues: 382 loop : -2.18 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 538 HIS 0.004 0.001 HIS E 286 PHE 0.018 0.001 PHE A 370 TYR 0.012 0.001 TYR H 235 ARG 0.006 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 157 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8258 (t80) REVERT: D 69 ARG cc_start: 0.7543 (mmm160) cc_final: 0.6873 (tpp-160) REVERT: E 263 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8284 (mptm) REVERT: F 40 MET cc_start: 0.2474 (OUTLIER) cc_final: 0.2200 (pmm) REVERT: F 84 LEU cc_start: 0.8358 (tp) cc_final: 0.8098 (tt) REVERT: F 118 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8343 (tmmm) REVERT: G 236 ASP cc_start: 0.7904 (t0) cc_final: 0.7253 (t0) REVERT: G 260 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: H 239 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8293 (mp10) REVERT: H 271 GLN cc_start: 0.8377 (mt0) cc_final: 0.8135 (mt0) outliers start: 82 outliers final: 33 residues processed: 223 average time/residue: 1.1131 time to fit residues: 282.0629 Evaluate side-chains 180 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 263 LYS Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 184 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN E 121 ASN F 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17643 Z= 0.188 Angle : 0.584 21.785 23918 Z= 0.280 Chirality : 0.043 0.288 2733 Planarity : 0.004 0.047 2929 Dihedral : 16.091 171.154 2997 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 4.86 % Allowed : 21.94 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 2045 helix: 0.97 (0.18), residues: 856 sheet: -0.51 (0.28), residues: 378 loop : -1.90 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.004 0.001 HIS E 286 PHE 0.018 0.001 PHE A 370 TYR 0.011 0.001 TYR A 239 ARG 0.004 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 156 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: A 365 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8118 (t80) REVERT: D 69 ARG cc_start: 0.7520 (mmm160) cc_final: 0.6797 (tpp-160) REVERT: E 263 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8318 (mmtm) REVERT: E 278 GLN cc_start: 0.7324 (tt0) cc_final: 0.7088 (pt0) REVERT: F 40 MET cc_start: 0.2185 (OUTLIER) cc_final: 0.1984 (pmm) REVERT: F 84 LEU cc_start: 0.8320 (tp) cc_final: 0.8085 (tt) REVERT: G 55 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: G 236 ASP cc_start: 0.7871 (t0) cc_final: 0.7269 (t0) REVERT: G 260 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: H 239 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8251 (mp10) REVERT: H 271 GLN cc_start: 0.8422 (mt0) cc_final: 0.8184 (mt0) outliers start: 87 outliers final: 40 residues processed: 221 average time/residue: 1.0625 time to fit residues: 267.9803 Evaluate side-chains 191 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 145 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 263 LYS Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 ASN G 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17643 Z= 0.205 Angle : 0.585 21.488 23918 Z= 0.280 Chirality : 0.043 0.273 2733 Planarity : 0.004 0.069 2929 Dihedral : 14.989 163.203 2991 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 4.58 % Allowed : 22.39 % Favored : 73.03 % 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: -0.37 (0.19), residues: 2045 helix: 1.22 (0.18), residues: 856 sheet: -0.37 (0.28), residues: 388 loop : -1.82 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.004 0.001 HIS E 302 PHE 0.018 0.001 PHE A 370 TYR 0.013 0.001 TYR E 66 ARG 0.015 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 154 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 352 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: D 69 ARG cc_start: 0.7558 (mmm160) cc_final: 0.6804 (tpp-160) REVERT: E 278 GLN cc_start: 0.7321 (tt0) cc_final: 0.7102 (pt0) REVERT: F 40 MET cc_start: 0.2138 (OUTLIER) cc_final: 0.1937 (ppp) REVERT: F 115 ASP cc_start: 0.7499 (m-30) cc_final: 0.7186 (m-30) REVERT: F 118 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8334 (tmmm) REVERT: G 55 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: G 236 ASP cc_start: 0.7862 (t0) cc_final: 0.7301 (t0) REVERT: G 260 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: H 239 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8218 (mp10) REVERT: H 271 GLN cc_start: 0.8422 (mt0) cc_final: 0.8177 (mt0) outliers start: 82 outliers final: 46 residues processed: 220 average time/residue: 0.9987 time to fit residues: 252.0923 Evaluate side-chains 196 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 ASN F 82 ASN F 224 ASN ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN G 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17643 Z= 0.421 Angle : 0.664 21.433 23918 Z= 0.324 Chirality : 0.047 0.401 2733 Planarity : 0.004 0.045 2929 Dihedral : 14.745 166.601 2990 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 5.64 % Allowed : 22.17 % Favored : 72.19 % 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: -0.48 (0.18), residues: 2045 helix: 1.11 (0.18), residues: 851 sheet: -0.47 (0.27), residues: 387 loop : -1.80 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 368 HIS 0.007 0.001 HIS E 302 PHE 0.022 0.002 PHE A 370 TYR 0.016 0.002 TYR E 255 ARG 0.007 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 141 time to evaluate : 1.962 Fit side-chains REVERT: A 352 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: D 69 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7044 (tpp-160) REVERT: E 278 GLN cc_start: 0.7316 (tt0) cc_final: 0.7090 (pt0) REVERT: F 40 MET cc_start: 0.2773 (OUTLIER) cc_final: 0.2466 (ppp) REVERT: F 118 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8307 (tmmm) REVERT: G 55 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: G 236 ASP cc_start: 0.7913 (t0) cc_final: 0.7367 (t0) REVERT: G 260 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: H 239 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8254 (mp10) outliers start: 101 outliers final: 49 residues processed: 219 average time/residue: 0.9807 time to fit residues: 247.5041 Evaluate side-chains 187 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 133 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 283 PHE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 104 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: G 32 GLN G 108 ASN G 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17643 Z= 0.173 Angle : 0.572 21.650 23918 Z= 0.277 Chirality : 0.042 0.253 2733 Planarity : 0.004 0.043 2929 Dihedral : 13.915 161.095 2988 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 3.85 % Allowed : 24.01 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2045 helix: 1.46 (0.18), residues: 849 sheet: -0.33 (0.28), residues: 386 loop : -1.67 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 538 HIS 0.003 0.001 HIS A 465 PHE 0.013 0.001 PHE A 365 TYR 0.015 0.001 TYR E 66 ARG 0.006 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 144 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: D 69 ARG cc_start: 0.7575 (mmm160) cc_final: 0.6842 (tpp-160) REVERT: E 307 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9035 (mp) REVERT: F 40 MET cc_start: 0.2485 (OUTLIER) cc_final: 0.2267 (ppp) REVERT: F 110 TYR cc_start: 0.6738 (m-80) cc_final: 0.6518 (m-80) REVERT: G 55 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: G 236 ASP cc_start: 0.7848 (t0) cc_final: 0.7323 (t0) REVERT: G 260 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: H 239 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8177 (mp10) outliers start: 69 outliers final: 42 residues processed: 202 average time/residue: 1.0823 time to fit residues: 250.8837 Evaluate side-chains 186 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 654 MET Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 166 optimal weight: 0.4980 chunk 110 optimal weight: 0.6980 chunk 197 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 GLN G 337 GLN H 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17643 Z= 0.149 Angle : 0.561 21.612 23918 Z= 0.268 Chirality : 0.042 0.348 2733 Planarity : 0.004 0.043 2929 Dihedral : 13.164 156.255 2987 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 3.57 % Allowed : 24.18 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 2045 helix: 1.62 (0.18), residues: 857 sheet: -0.15 (0.28), residues: 384 loop : -1.59 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 208 HIS 0.003 0.001 HIS A 465 PHE 0.013 0.001 PHE A 365 TYR 0.013 0.001 TYR E 66 ARG 0.006 0.000 ARG H 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 151 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 69 ARG cc_start: 0.7554 (mmm160) cc_final: 0.6866 (tpp-160) REVERT: F 110 TYR cc_start: 0.6619 (m-80) cc_final: 0.6388 (m-80) REVERT: G 55 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: G 236 ASP cc_start: 0.7794 (t0) cc_final: 0.7314 (t0) REVERT: G 260 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6323 (mp0) REVERT: H 239 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8122 (mp10) outliers start: 64 outliers final: 39 residues processed: 200 average time/residue: 1.0459 time to fit residues: 238.9868 Evaluate side-chains 184 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 348 ASP Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17643 Z= 0.175 Angle : 0.590 21.628 23918 Z= 0.282 Chirality : 0.043 0.272 2733 Planarity : 0.004 0.046 2929 Dihedral : 12.862 155.134 2986 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 3.57 % Allowed : 24.46 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2045 helix: 1.66 (0.18), residues: 863 sheet: -0.06 (0.28), residues: 379 loop : -1.58 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 538 HIS 0.004 0.001 HIS A 465 PHE 0.013 0.001 PHE A 365 TYR 0.015 0.001 TYR E 114 ARG 0.011 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 143 time to evaluate : 2.016 Fit side-chains revert: symmetry clash REVERT: D 69 ARG cc_start: 0.7519 (mmm160) cc_final: 0.6843 (tpp-160) REVERT: E 307 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9025 (mp) REVERT: F 40 MET cc_start: 0.1969 (ppp) cc_final: 0.1697 (pmt) REVERT: F 110 TYR cc_start: 0.6588 (m-80) cc_final: 0.6348 (m-80) REVERT: G 55 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: G 236 ASP cc_start: 0.7787 (t0) cc_final: 0.7314 (t0) REVERT: G 260 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6265 (mp0) REVERT: H 239 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8126 (mp10) outliers start: 64 outliers final: 42 residues processed: 193 average time/residue: 1.0537 time to fit residues: 233.1078 Evaluate side-chains 182 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 0.0570 chunk 166 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17643 Z= 0.158 Angle : 0.586 21.685 23918 Z= 0.278 Chirality : 0.042 0.261 2733 Planarity : 0.004 0.043 2929 Dihedral : 12.375 152.317 2985 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 2.62 % Allowed : 25.40 % Favored : 71.97 % 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: 0.28 (0.19), residues: 2045 helix: 1.76 (0.18), residues: 863 sheet: -0.00 (0.28), residues: 379 loop : -1.51 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 208 HIS 0.003 0.001 HIS A 465 PHE 0.013 0.001 PHE A 365 TYR 0.011 0.001 TYR H 235 ARG 0.005 0.000 ARG H 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.942 Fit side-chains REVERT: D 69 ARG cc_start: 0.7493 (mmm160) cc_final: 0.6847 (tpp-160) REVERT: F 40 MET cc_start: 0.1948 (ppp) cc_final: 0.1714 (pmt) REVERT: F 110 TYR cc_start: 0.6669 (m-80) cc_final: 0.6441 (m-80) REVERT: F 153 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6436 (mtp180) REVERT: G 55 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6771 (tm-30) REVERT: G 236 ASP cc_start: 0.7749 (t0) cc_final: 0.7299 (t0) REVERT: G 260 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: H 239 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8109 (mp10) outliers start: 47 outliers final: 39 residues processed: 182 average time/residue: 1.0814 time to fit residues: 225.8768 Evaluate side-chains 178 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 204 optimal weight: 0.3980 chunk 187 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17643 Z= 0.167 Angle : 0.596 21.692 23918 Z= 0.281 Chirality : 0.042 0.260 2733 Planarity : 0.004 0.049 2929 Dihedral : 12.119 151.059 2985 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 2.62 % Allowed : 25.63 % Favored : 71.75 % 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: 0.34 (0.19), residues: 2045 helix: 1.80 (0.18), residues: 862 sheet: 0.05 (0.29), residues: 379 loop : -1.47 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP E 208 HIS 0.004 0.001 HIS A 465 PHE 0.013 0.001 PHE A 365 TYR 0.017 0.001 TYR H 299 ARG 0.006 0.000 ARG F 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 1.885 Fit side-chains REVERT: A 528 ASP cc_start: 0.8424 (t0) cc_final: 0.8179 (t0) REVERT: D 69 ARG cc_start: 0.7472 (mmm160) cc_final: 0.6801 (tpp-160) REVERT: F 40 MET cc_start: 0.2011 (ppp) cc_final: 0.1725 (pmt) REVERT: F 110 TYR cc_start: 0.6728 (m-80) cc_final: 0.6491 (m-80) REVERT: F 115 ASP cc_start: 0.7482 (m-30) cc_final: 0.7085 (m-30) REVERT: F 118 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8369 (tmmm) REVERT: F 125 GLN cc_start: 0.8464 (mt0) cc_final: 0.8164 (pt0) REVERT: F 138 LEU cc_start: 0.8087 (tt) cc_final: 0.7604 (pp) REVERT: F 153 ARG cc_start: 0.6890 (mtp85) cc_final: 0.6375 (mtp180) REVERT: G 55 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: G 236 ASP cc_start: 0.7747 (t0) cc_final: 0.7297 (t0) REVERT: G 260 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: H 239 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8130 (mp10) outliers start: 47 outliers final: 41 residues processed: 178 average time/residue: 1.0737 time to fit residues: 218.4541 Evaluate side-chains 182 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 82 ASN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 45 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 167 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 143 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.084377 restraints weight = 27760.266| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.23 r_work: 0.2934 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17643 Z= 0.140 Angle : 0.581 21.680 23918 Z= 0.273 Chirality : 0.042 0.249 2733 Planarity : 0.004 0.043 2929 Dihedral : 11.491 146.133 2985 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.07 % Allowed : 26.07 % Favored : 71.86 % 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: 0.45 (0.19), residues: 2045 helix: 1.91 (0.18), residues: 863 sheet: 0.08 (0.29), residues: 384 loop : -1.44 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP E 208 HIS 0.004 0.001 HIS A 465 PHE 0.013 0.001 PHE G 355 TYR 0.016 0.001 TYR E 114 ARG 0.006 0.000 ARG H 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5437.33 seconds wall clock time: 97 minutes 46.80 seconds (5866.80 seconds total)