Starting phenix.real_space_refine on Sat Jul 4 03:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.map 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/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.map" model { file = "/net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8agb_15419/07_2026/8agb_15419.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'ASP:plan': 4, 'ASN:plan1': 1} 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 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 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 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 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 chiralities: 2 Time building chain proxies: 3.76, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 1.91 Conformation dependent library (CDL) restraints added in 734.8 milliseconds 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... Secondary structure from input PDB file: 64 helices and 20 sheets defined 46.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 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 45 through 61 removed outlier: 3.689A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.755A pdb=" N LEU A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 117 through 138 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 139 through 153 removed outlier: 4.037A pdb=" N ILE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 removed outlier: 4.824A pdb=" N ARG A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 189 removed outlier: 4.236A pdb=" N ILE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) 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 190 through 206 removed outlier: 3.550A pdb=" N ALA A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.578A pdb=" N TYR A 211 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 213 through 228 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 232 through 251 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) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 289 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 355 through 363 removed outlier: 4.296A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 381 removed outlier: 4.286A pdb=" N LEU A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Proline residue: A 371 - end of helix removed outlier: 3.812A pdb=" N ASP A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.645A pdb=" N VAL A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 429 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 441 through 473 removed outlier: 3.702A pdb=" N LEU A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 506 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 553 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 586 through 594 Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.571A pdb=" N PHE A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 627 through 634 removed outlier: 3.700A pdb=" N LYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.615A pdb=" N PHE A 641 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN A 642 " --> pdb=" O GLN A 639 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 643 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN A 645 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.857A pdb=" N VAL A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'B' and resid 3 through 32 removed outlier: 3.522A pdb=" N LEU B 7 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 47 removed outlier: 3.620A pdb=" N PHE C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 82 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 41 Processing helix chain 'D' and resid 41 through 69 removed outlier: 3.965A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 100 Processing helix chain 'D' and resid 106 through 129 removed outlier: 3.603A pdb=" N PHE D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 3.609A pdb=" N LYS E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 Processing helix chain 'E' and resid 442 through 447 Processing helix chain 'E' and resid 447 through 469 removed outlier: 3.558A pdb=" N LEU E 451 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 193 through 217 removed outlier: 3.503A pdb=" N ALA F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) 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 231 through 254 removed outlier: 3.826A pdb=" N GLY F 237 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 283 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 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 50 removed outlier: 3.694A pdb=" N LEU G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 211 through 215 removed outlier: 4.135A pdb=" N GLN G 214 " --> pdb=" O SER G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 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 385 through 389 removed outlier: 3.573A pdb=" N ILE G 389 " --> pdb=" O SER G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 392 through 416 removed outlier: 3.605A pdb=" N VAL G 411 " --> pdb=" O ILE G 407 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR G 416 " --> pdb=" O SER G 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 233 Processing helix chain 'H' and resid 235 through 241 removed outlier: 3.682A pdb=" N GLN H 239 " --> pdb=" O TYR H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 289 removed outlier: 3.940A pdb=" N GLN H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL H 274 " --> pdb=" O THR H 270 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU H 275 " --> pdb=" O GLN H 271 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 282 " --> pdb=" O GLY H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 299 removed outlier: 3.541A pdb=" N ARG H 295 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 513 through 514 removed outlier: 6.510A pdb=" N ALA A 514 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ILE A 572 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 677 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR A 671 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 679 " --> pdb=" O VAL A 669 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 646 through 647 Processing sheet with id=AA3, first strand: chain 'E' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'E' and resid 80 through 85 removed outlier: 3.520A pdb=" N PHE E 80 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 48 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR E 176 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG E 38 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE E 178 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE E 40 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 204 " --> pdb=" O LYS E 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 63 through 70 removed outlier: 6.187A pdb=" N THR E 64 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN E 93 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.728A pdb=" N GLN E 154 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 147 through 148 Processing sheet with id=AA8, first strand: chain 'E' and resid 231 through 236 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 231 through 236 current: chain 'E' and resid 248 through 259 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 248 through 259 current: chain 'E' and resid 334 through 344 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 334 through 344 current: chain 'E' and resid 416 through 423 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 291 through 294 Processing sheet with id=AB1, first strand: chain 'E' and resid 349 through 351 removed outlier: 6.766A pdb=" N LEU E 436 " --> pdb=" O ILE E 392 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE E 392 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS E 438 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.537A pdb=" N ASN F 70 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE F 114 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA F 34 " --> pdb=" O ILE F 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 43 through 44 removed outlier: 5.480A pdb=" N PHE F 152 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU F 140 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N GLU F 154 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 138 " --> pdb=" O GLU F 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 100 through 101 removed outlier: 4.270A pdb=" N GLU F 100 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS F 111 " --> pdb=" O GLU F 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 26 through 28 removed outlier: 6.476A pdb=" N THR G 26 " --> pdb=" O GLU G 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.730A pdb=" N MET G 112 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE G 109 " --> pdb=" O VAL G 230 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE G 232 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS G 111 " --> pdb=" O ILE G 232 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AB8, 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=AB9, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AC1, first strand: chain 'G' and resid 263 through 273 removed outlier: 6.023A pdb=" N ILE G 264 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 299 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER G 266 " --> pdb=" O SER G 297 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER G 297 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N HIS G 268 " --> pdb=" O GLY G 295 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY G 295 " --> pdb=" O HIS G 268 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 304 through 306 current: chain 'G' and resid 337 through 340 Processing sheet with id=AC2, first strand: chain 'G' and resid 321 through 326 removed outlier: 5.117A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2220 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: 2.91 Time building geometry restraints manager: 2.34 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=" O3A ELU A 804 " pdb=" PB ELU A 804 " ideal model delta sigma weight residual 1.747 1.645 0.102 2.00e-02 2.50e+03 2.59e+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 ... (remaining 17638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 23607 3.49 - 6.98: 264 6.98 - 10.47: 40 10.47 - 13.96: 3 13.96 - 17.45: 4 Bond angle restraints: 23918 Sorted by residual: 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 angle pdb=" O3P CPL B 101 " pdb=" P CPL B 101 " pdb=" O4P CPL B 101 " ideal model delta sigma weight residual 93.29 109.92 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O11 PTY A 802 " pdb=" P1 PTY A 802 " pdb=" O14 PTY A 802 " ideal model delta sigma weight residual 92.90 109.01 -16.11 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O11 PTY F 301 " pdb=" P1 PTY F 301 " pdb=" O14 PTY F 301 " ideal model delta sigma weight residual 92.90 108.59 -15.69 3.00e+00 1.11e-01 2.73e+01 ... (remaining 23913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.53: 9628 30.53 - 61.05: 501 61.05 - 91.58: 28 91.58 - 122.11: 3 122.11 - 152.63: 3 Dihedral angle restraints: 10163 sinusoidal: 4075 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=" N1 PTY F 301 " pdb=" C2 PTY F 301 " pdb=" C3 PTY F 301 " pdb=" O11 PTY F 301 " ideal model delta sinusoidal sigma weight residual 65.33 -142.04 -152.63 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 10160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2282 0.061 - 0.123: 384 0.123 - 0.184: 52 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: 169 2.62 - 3.19: 15264 3.19 - 3.76: 24909 3.76 - 4.33: 36821 4.33 - 4.90: 61341 Nonbonded interactions: 138504 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 3.040 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 3.040 nonbonded pdb=" OD1 ASP A 110 " pdb=" N ILE A 111 " model vdw 2.272 3.120 ... (remaining 138499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 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 17668 Z= 0.291 Angle : 0.919 17.450 23990 Z= 0.440 Chirality : 0.050 0.307 2733 Planarity : 0.008 0.235 2929 Dihedral : 17.255 152.633 6229 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.51 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG A 615 TYR 0.012 0.001 TYR A 501 PHE 0.029 0.001 PHE C 45 TRP 0.027 0.002 TRP A 368 HIS 0.004 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.29 (17643) covalent geometry : angle 0.91369 / 0.44 (23918) hydrogen bonds : bond 0.15131 / 10.02 ( 765) hydrogen bonds : angle 6.46007 / 4.67 ( 2220) Misc. bond : bond 0.00045 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00278 / 0.14 ( 5) link_ALPHA1-2 : angle 2.25415 / 1.28 ( 15) link_ALPHA1-3 : bond 0.00633 / 0.37 ( 5) link_ALPHA1-3 : angle 1.61082 / 1.09 ( 15) link_ALPHA1-6 : bond 0.00496 / 0.24 ( 2) link_ALPHA1-6 : angle 1.74424 / 0.96 ( 6) link_BETA1-4 : bond 0.00388 / 0.24 ( 7) link_BETA1-4 : angle 1.92559 / 1.11 ( 21) link_NAG-ASN : bond 0.00339 / 0.17 ( 5) link_NAG-ASN : angle 2.26031 / 1.48 ( 15) *********************** 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 to be fit. rotamer outliers: 108 poor density : 184 time to evaluate : 0.639 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: 0.8320 (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: 0.5184 time to fit residues: 163.6907 Evaluate side-chains 186 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 266 HIS A 277 GLN A 506 ASN A 653 GLN A 688 GLN B 8 ASN 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 F 82 ASN F 90 ASN F 104 ASN F 159 ASN F 166 HIS F 217 ASN G 157 HIS G 214 GLN G 226 ASN G 242 ASN G 243 GLN G 246 ASN G 271 HIS G 273 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.081986 restraints weight = 27954.960| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.22 r_work: 0.2882 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17668 Z= 0.131 Angle : 0.585 6.760 23990 Z= 0.299 Chirality : 0.044 0.322 2733 Planarity : 0.004 0.045 2929 Dihedral : 12.052 154.234 2534 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 4.75 % Allowed : 21.55 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.18), residues: 2045 helix: 0.52 (0.18), residues: 857 sheet: -1.02 (0.26), residues: 388 loop : -2.11 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.013 0.001 TYR G 143 PHE 0.019 0.001 PHE A 370 TRP 0.016 0.001 TRP A 538 HIS 0.003 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17643) covalent geometry : angle 0.57832 / 0.30 (23918) hydrogen bonds : bond 0.05038 / 3.39 ( 765) hydrogen bonds : angle 4.56892 / 3.29 ( 2220) Misc. bond : bond 0.00008 / 0.00 ( 1) link_ALPHA1-2 : bond 0.00214 / 0.13 ( 5) link_ALPHA1-2 : angle 1.91571 / 1.08 ( 15) link_ALPHA1-3 : bond 0.00716 / 0.43 ( 5) link_ALPHA1-3 : angle 1.33471 / 0.88 ( 15) link_ALPHA1-6 : bond 0.00486 / 0.23 ( 2) link_ALPHA1-6 : angle 1.85396 / 1.01 ( 6) link_BETA1-4 : bond 0.00404 / 0.24 ( 7) link_BETA1-4 : angle 1.52580 / 0.97 ( 21) link_NAG-ASN : bond 0.00593 / 0.31 ( 5) link_NAG-ASN : angle 2.09567 / 1.31 ( 15) *********************** 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 244 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 159 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8362 (t80) REVERT: A 647 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8866 (m) REVERT: C 5 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7972 (tm-30) REVERT: C 8 LYS cc_start: 0.8841 (tppt) cc_final: 0.8616 (ptmt) REVERT: D 69 ARG cc_start: 0.7503 (mmm160) cc_final: 0.6321 (tpp-160) REVERT: E 58 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (mp) REVERT: E 266 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7610 (pptt) REVERT: E 317 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: F 40 MET cc_start: 0.2865 (OUTLIER) cc_final: 0.2398 (ppp) REVERT: F 84 LEU cc_start: 0.8358 (tp) cc_final: 0.8036 (tt) REVERT: F 118 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8254 (tmmm) REVERT: G 73 GLN cc_start: 0.7308 (pp30) cc_final: 0.7096 (pp30) REVERT: G 141 ARG cc_start: 0.7761 (mmp80) cc_final: 0.7524 (mmp80) REVERT: G 196 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7254 (mtp180) REVERT: G 236 ASP cc_start: 0.8689 (t0) cc_final: 0.7846 (t0) REVERT: G 260 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: H 239 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7967 (mp10) REVERT: H 260 ASN cc_start: 0.9049 (t0) cc_final: 0.8816 (t0) REVERT: H 271 GLN cc_start: 0.8702 (mt0) cc_final: 0.8500 (mt0) outliers start: 85 outliers final: 30 residues processed: 232 average time/residue: 0.4925 time to fit residues: 130.6615 Evaluate side-chains 186 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 446 LEU 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 A residue 647 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 317 GLU 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 103 ASP Chi-restraints excluded: chain F residue 118 LYS 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 G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 260 GLU 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 107 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 41 optimal weight: 0.0070 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 ASN F 82 ASN F 159 ASN G 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.083931 restraints weight = 28476.534| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.09 r_work: 0.2904 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17668 Z= 0.114 Angle : 0.533 6.283 23990 Z= 0.271 Chirality : 0.042 0.312 2733 Planarity : 0.004 0.046 2929 Dihedral : 10.625 157.097 2483 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.72 % Rotamer: Outliers : 4.02 % Allowed : 22.45 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 2045 helix: 1.37 (0.18), residues: 861 sheet: -0.61 (0.27), residues: 382 loop : -1.75 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 159 TYR 0.012 0.001 TYR A 501 PHE 0.017 0.001 PHE A 370 TRP 0.013 0.001 TRP A 538 HIS 0.003 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17643) covalent geometry : angle 0.52473 / 0.27 (23918) hydrogen bonds : bond 0.04356 / 2.90 ( 765) hydrogen bonds : angle 4.16625 / 3.00 ( 2220) Misc. bond : bond 0.00020 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00285 / 0.15 ( 5) link_ALPHA1-2 : angle 1.72705 / 0.99 ( 15) link_ALPHA1-3 : bond 0.00726 / 0.45 ( 5) link_ALPHA1-3 : angle 1.24080 / 0.82 ( 15) link_ALPHA1-6 : bond 0.00509 / 0.24 ( 2) link_ALPHA1-6 : angle 1.67877 / 0.91 ( 6) link_BETA1-4 : bond 0.00394 / 0.22 ( 7) link_BETA1-4 : angle 1.51137 / 0.95 ( 21) link_NAG-ASN : bond 0.00799 / 0.41 ( 5) link_NAG-ASN : angle 2.43321 / 1.56 ( 15) *********************** 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 236 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 164 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8316 (t80) REVERT: C 5 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8076 (tm-30) REVERT: D 69 ARG cc_start: 0.7699 (mmm160) cc_final: 0.6649 (tpp-160) REVERT: D 70 ASP cc_start: 0.8463 (t70) cc_final: 0.8239 (t0) REVERT: E 58 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7682 (mp) REVERT: E 243 SER cc_start: 0.9293 (OUTLIER) cc_final: 0.9048 (p) REVERT: E 266 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7663 (pptt) REVERT: E 279 THR cc_start: 0.7679 (p) cc_final: 0.7165 (t) REVERT: F 84 LEU cc_start: 0.8352 (tp) cc_final: 0.8099 (tt) REVERT: G 55 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: G 97 LYS cc_start: 0.8435 (tppt) cc_final: 0.8155 (mptt) REVERT: G 196 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7400 (mtp85) REVERT: G 236 ASP cc_start: 0.8623 (t0) cc_final: 0.7939 (t0) REVERT: G 260 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: H 239 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8343 (mp10) REVERT: H 295 ARG cc_start: 0.7504 (tmm-80) cc_final: 0.7241 (tmm-80) REVERT: H 303 LYS cc_start: 0.7605 (pttp) cc_final: 0.7365 (pttp) outliers start: 72 outliers final: 31 residues processed: 220 average time/residue: 0.4912 time to fit residues: 123.3900 Evaluate side-chains 186 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 ILE 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 445 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE 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 243 SER Chi-restraints excluded: chain E residue 289 THR 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 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 G residue 27 LEU 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 202 SER Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 407 ILE 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 97 optimal weight: 8.9990 chunk 126 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 156 optimal weight: 0.3980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 108 ASN F 82 ASN F 159 ASN G 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081606 restraints weight = 28438.710| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.16 r_work: 0.2861 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17668 Z= 0.161 Angle : 0.556 7.993 23990 Z= 0.281 Chirality : 0.044 0.347 2733 Planarity : 0.004 0.065 2929 Dihedral : 10.418 162.751 2479 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 4.75 % Allowed : 21.78 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 2045 helix: 1.60 (0.17), residues: 861 sheet: -0.53 (0.27), residues: 386 loop : -1.65 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 213 TYR 0.013 0.001 TYR A 239 PHE 0.020 0.001 PHE A 370 TRP 0.012 0.001 TRP A 368 HIS 0.004 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (17643) covalent geometry : angle 0.54588 / 0.28 (23918) hydrogen bonds : bond 0.04737 / 3.16 ( 765) hydrogen bonds : angle 4.13762 / 2.97 ( 2220) Misc. bond : bond 0.00025 / 0.01 ( 1) link_ALPHA1-2 : bond 0.00251 / 0.13 ( 5) link_ALPHA1-2 : angle 1.75653 / 1.02 ( 15) link_ALPHA1-3 : bond 0.00670 / 0.41 ( 5) link_ALPHA1-3 : angle 1.31461 / 0.89 ( 15) link_ALPHA1-6 : bond 0.00600 / 0.29 ( 2) link_ALPHA1-6 : angle 1.77422 / 0.97 ( 6) link_BETA1-4 : bond 0.00291 / 0.15 ( 7) link_BETA1-4 : angle 1.68016 / 1.02 ( 21) link_NAG-ASN : bond 0.00268 / 0.16 ( 5) link_NAG-ASN : angle 2.92781 / 1.91 ( 15) *********************** 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 240 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 155 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8038 (mtm110) REVERT: A 352 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6901 (pm20) REVERT: A 402 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: C 5 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8069 (tm-30) REVERT: D 69 ARG cc_start: 0.7793 (mmm160) cc_final: 0.6740 (tpp-160) REVERT: D 70 ASP cc_start: 0.8493 (t70) cc_final: 0.8286 (t0) REVERT: E 58 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7673 (mp) REVERT: E 243 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.9062 (p) REVERT: E 266 LYS cc_start: 0.7897 (mmtm) cc_final: 0.7689 (pptt) REVERT: F 40 MET cc_start: 0.2696 (OUTLIER) cc_final: 0.1436 (pmt) REVERT: F 84 LEU cc_start: 0.8343 (tp) cc_final: 0.8143 (tt) REVERT: F 118 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8273 (tmmm) REVERT: G 55 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: G 97 LYS cc_start: 0.8482 (tppt) cc_final: 0.8184 (mptt) REVERT: G 196 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7411 (ttp80) REVERT: G 236 ASP cc_start: 0.8653 (t0) cc_final: 0.7967 (t0) REVERT: G 260 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: G 335 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7173 (mm-30) REVERT: H 239 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8327 (mp10) outliers start: 85 outliers final: 43 residues processed: 219 average time/residue: 0.4905 time to fit residues: 122.0603 Evaluate side-chains 200 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 THR Chi-restraints excluded: chain A residue 262 ARG 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 402 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE 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 243 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL 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 103 ASP Chi-restraints excluded: chain F residue 118 LYS 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 G residue 27 LEU Chi-restraints excluded: chain G residue 29 LEU 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 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 84 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 ASN E 280 GLN F 82 ASN F 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.082329 restraints weight = 27947.584| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.21 r_work: 0.2884 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17668 Z= 0.117 Angle : 0.531 7.508 23990 Z= 0.268 Chirality : 0.042 0.348 2733 Planarity : 0.004 0.043 2929 Dihedral : 9.982 165.937 2478 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 4.19 % Allowed : 22.67 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 2045 helix: 1.88 (0.18), residues: 863 sheet: -0.48 (0.27), residues: 397 loop : -1.56 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 213 TYR 0.015 0.001 TYR G 143 PHE 0.017 0.001 PHE A 370 TRP 0.011 0.001 TRP A 538 HIS 0.004 0.001 HIS H 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17643) covalent geometry : angle 0.52187 / 0.27 (23918) hydrogen bonds : bond 0.04274 / 2.85 ( 765) hydrogen bonds : angle 3.99647 / 2.88 ( 2220) Misc. bond : bond 0.00029 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00203 / 0.13 ( 5) link_ALPHA1-2 : angle 1.67700 / 0.98 ( 15) link_ALPHA1-3 : bond 0.00707 / 0.42 ( 5) link_ALPHA1-3 : angle 1.22294 / 0.82 ( 15) link_ALPHA1-6 : bond 0.00657 / 0.32 ( 2) link_ALPHA1-6 : angle 1.78259 / 0.96 ( 6) link_BETA1-4 : bond 0.00342 / 0.19 ( 7) link_BETA1-4 : angle 1.54134 / 0.95 ( 21) link_NAG-ASN : bond 0.00387 / 0.21 ( 5) link_NAG-ASN : angle 2.81928 / 1.83 ( 15) *********************** 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 229 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 154 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7804 (mtm110) REVERT: A 352 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6583 (pm20) REVERT: B 1 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7559 (ttt) REVERT: D 69 ARG cc_start: 0.7536 (mmm160) cc_final: 0.6403 (tpp-160) REVERT: D 70 ASP cc_start: 0.8404 (t70) cc_final: 0.8191 (t0) REVERT: E 243 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.9007 (p) REVERT: E 266 LYS cc_start: 0.7901 (mmtm) cc_final: 0.7577 (pptt) REVERT: E 393 ASP cc_start: 0.8611 (m-30) cc_final: 0.8313 (m-30) REVERT: F 40 MET cc_start: 0.2513 (OUTLIER) cc_final: 0.1289 (pmt) REVERT: F 84 LEU cc_start: 0.8252 (tp) cc_final: 0.8034 (tt) REVERT: F 113 ARG cc_start: 0.8057 (ptt-90) cc_final: 0.7800 (ptp-170) REVERT: F 118 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8233 (tmmm) REVERT: G 55 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: G 97 LYS cc_start: 0.8311 (tppt) cc_final: 0.7991 (mptt) REVERT: G 196 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7235 (mtp85) REVERT: G 236 ASP cc_start: 0.8648 (t0) cc_final: 0.7901 (t0) REVERT: G 260 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: G 335 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6911 (mm-30) REVERT: G 381 ASP cc_start: 0.8573 (t0) cc_final: 0.8361 (t0) REVERT: H 239 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8054 (mp10) outliers start: 75 outliers final: 34 residues processed: 210 average time/residue: 0.4989 time to fit residues: 119.1132 Evaluate side-chains 189 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 262 ARG 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 655 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 208 TRP Chi-restraints excluded: chain E residue 243 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 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 186 HIS Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 111 CYS Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 260 GLU 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 197 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.081858 restraints weight = 27734.121| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.22 r_work: 0.2876 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17668 Z= 0.122 Angle : 0.535 7.730 23990 Z= 0.269 Chirality : 0.042 0.314 2733 Planarity : 0.004 0.043 2929 Dihedral : 9.741 168.715 2475 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 4.19 % Allowed : 22.67 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 2045 helix: 2.03 (0.18), residues: 863 sheet: -0.41 (0.27), residues: 397 loop : -1.50 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 213 TYR 0.015 0.001 TYR E 66 PHE 0.017 0.001 PHE A 370 TRP 0.010 0.001 TRP A 538 HIS 0.004 0.001 HIS H 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (17643) covalent geometry : angle 0.52650 / 0.27 (23918) hydrogen bonds : bond 0.04249 / 2.83 ( 765) hydrogen bonds : angle 3.94264 / 2.83 ( 2220) Misc. bond : bond 0.00032 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00166 / 0.10 ( 5) link_ALPHA1-2 : angle 1.68551 / 0.99 ( 15) link_ALPHA1-3 : bond 0.00682 / 0.41 ( 5) link_ALPHA1-3 : angle 1.24228 / 0.83 ( 15) link_ALPHA1-6 : bond 0.00612 / 0.29 ( 2) link_ALPHA1-6 : angle 1.72318 / 0.93 ( 6) link_BETA1-4 : bond 0.00314 / 0.17 ( 7) link_BETA1-4 : angle 1.57316 / 0.96 ( 21) link_NAG-ASN : bond 0.00333 / 0.19 ( 5) link_NAG-ASN : angle 2.44213 / 1.58 ( 15) *********************** 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 229 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 154 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7829 (mtm110) REVERT: A 352 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: B 1 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: D 69 ARG cc_start: 0.7521 (mmm160) cc_final: 0.6385 (tpp-160) REVERT: E 266 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7572 (pptt) REVERT: E 393 ASP cc_start: 0.8633 (m-30) cc_final: 0.8305 (m-30) REVERT: F 40 MET cc_start: 0.2319 (OUTLIER) cc_final: 0.1669 (pmt) REVERT: F 84 LEU cc_start: 0.8320 (tp) cc_final: 0.8036 (tt) REVERT: F 103 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6316 (p0) REVERT: F 113 ARG cc_start: 0.8032 (ptt-90) cc_final: 0.7617 (ptp-170) REVERT: F 118 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8249 (tmmm) REVERT: G 49 GLN cc_start: 0.8509 (mm110) cc_final: 0.8230 (mm110) REVERT: G 55 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: G 97 LYS cc_start: 0.8337 (tppt) cc_final: 0.8017 (mptt) REVERT: G 196 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7266 (mtp85) REVERT: G 236 ASP cc_start: 0.8651 (t0) cc_final: 0.7923 (t0) REVERT: G 260 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: G 335 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6905 (mm-30) REVERT: G 381 ASP cc_start: 0.8555 (t0) cc_final: 0.8285 (t0) REVERT: H 239 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8058 (mp10) outliers start: 75 outliers final: 42 residues processed: 212 average time/residue: 0.5197 time to fit residues: 125.2688 Evaluate side-chains 196 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 262 ARG 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 545 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE 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 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL 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 118 LYS Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 VAL 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 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 55 optimal weight: 2.9990 chunk 140 optimal weight: 0.0060 chunk 18 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 178 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.9776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 ASN F 82 ASN F 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082244 restraints weight = 27950.697| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.23 r_work: 0.2882 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17668 Z= 0.126 Angle : 0.543 9.545 23990 Z= 0.271 Chirality : 0.043 0.444 2733 Planarity : 0.004 0.043 2929 Dihedral : 9.563 172.904 2474 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 3.74 % Allowed : 23.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.19), residues: 2045 helix: 2.13 (0.17), residues: 863 sheet: -0.32 (0.28), residues: 386 loop : -1.51 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 619 TYR 0.014 0.001 TYR E 114 PHE 0.017 0.001 PHE A 370 TRP 0.010 0.001 TRP A 538 HIS 0.004 0.001 HIS H 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (17643) covalent geometry : angle 0.53299 / 0.27 (23918) hydrogen bonds : bond 0.04262 / 2.84 ( 765) hydrogen bonds : angle 3.91901 / 2.82 ( 2220) Misc. bond : bond 0.00034 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00190 / 0.12 ( 5) link_ALPHA1-2 : angle 1.67424 / 0.99 ( 15) link_ALPHA1-3 : bond 0.00674 / 0.40 ( 5) link_ALPHA1-3 : angle 1.24305 / 0.84 ( 15) link_ALPHA1-6 : bond 0.00591 / 0.28 ( 2) link_ALPHA1-6 : angle 1.72704 / 0.94 ( 6) link_BETA1-4 : bond 0.00307 / 0.17 ( 7) link_BETA1-4 : angle 1.59779 / 0.97 ( 21) link_NAG-ASN : bond 0.00356 / 0.20 ( 5) link_NAG-ASN : angle 3.04378 / 1.98 ( 15) *********************** 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 217 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 150 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7795 (mtm110) REVERT: A 352 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: B 1 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7624 (ttt) REVERT: D 69 ARG cc_start: 0.7490 (mmm160) cc_final: 0.6359 (tpp-160) REVERT: E 243 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9008 (p) REVERT: E 266 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7578 (pptt) REVERT: E 393 ASP cc_start: 0.8608 (m-30) cc_final: 0.8343 (m-30) REVERT: F 40 MET cc_start: 0.2422 (OUTLIER) cc_final: 0.1701 (pmt) REVERT: F 84 LEU cc_start: 0.8235 (tp) cc_final: 0.8024 (tt) REVERT: F 113 ARG cc_start: 0.8052 (ptt-90) cc_final: 0.7837 (ptp-170) REVERT: F 118 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8244 (tmmm) REVERT: G 49 GLN cc_start: 0.8507 (mm110) cc_final: 0.8244 (mm110) REVERT: G 55 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: G 97 LYS cc_start: 0.8321 (tppt) cc_final: 0.7992 (mptt) REVERT: G 196 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7199 (mtp85) REVERT: G 236 ASP cc_start: 0.8597 (t0) cc_final: 0.7878 (t0) REVERT: G 260 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: G 335 GLU cc_start: 0.7584 (mt-10) cc_final: 0.6939 (mm-30) REVERT: G 381 ASP cc_start: 0.8596 (t0) cc_final: 0.8299 (t0) REVERT: H 239 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8052 (mp10) outliers start: 67 outliers final: 41 residues processed: 201 average time/residue: 0.5458 time to fit residues: 124.5117 Evaluate side-chains 194 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 262 ARG 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 545 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE 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 208 TRP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL 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 118 LYS Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 VAL 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 260 GLU Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain H residue 284 VAL Chi-restraints excluded: chain H residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 39 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 ASN F 82 ASN F 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.081796 restraints weight = 28126.062| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.23 r_work: 0.2874 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 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 : 0.003 0.045 17668 Z= 0.137 Angle : 0.553 9.173 23990 Z= 0.276 Chirality : 0.043 0.317 2733 Planarity : 0.004 0.043 2929 Dihedral : 9.426 176.125 2471 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 3.69 % Allowed : 23.67 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.19), residues: 2045 helix: 2.17 (0.17), residues: 863 sheet: -0.29 (0.28), residues: 385 loop : -1.50 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 74 TYR 0.016 0.001 TYR A 501 PHE 0.019 0.001 PHE G 76 TRP 0.010 0.001 TRP A 368 HIS 0.004 0.001 HIS E 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17643) covalent geometry : angle 0.54457 / 0.27 (23918) hydrogen bonds : bond 0.04357 / 2.90 ( 765) hydrogen bonds : angle 3.92643 / 2.82 ( 2220) Misc. bond : bond 0.00036 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00190 / 0.11 ( 5) link_ALPHA1-2 : angle 1.68518 / 0.99 ( 15) link_ALPHA1-3 : bond 0.00670 / 0.40 ( 5) link_ALPHA1-3 : angle 1.26165 / 0.85 ( 15) link_ALPHA1-6 : bond 0.00578 / 0.28 ( 2) link_ALPHA1-6 : angle 1.73278 / 0.94 ( 6) link_BETA1-4 : bond 0.00289 / 0.16 ( 7) link_BETA1-4 : angle 1.62196 / 0.98 ( 21) link_NAG-ASN : bond 0.00326 / 0.19 ( 5) link_NAG-ASN : angle 2.66343 / 1.73 ( 15) *********************** 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 214 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 148 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7776 (mtm110) REVERT: A 352 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6607 (pm20) REVERT: B 1 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7650 (ttt) REVERT: D 69 ARG cc_start: 0.7562 (mmm160) cc_final: 0.6444 (tpp-160) REVERT: E 243 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8999 (p) REVERT: E 266 LYS cc_start: 0.7892 (mmtm) cc_final: 0.7592 (pptt) REVERT: E 393 ASP cc_start: 0.8625 (m-30) cc_final: 0.8352 (m-30) REVERT: F 84 LEU cc_start: 0.8185 (tp) cc_final: 0.7976 (tt) REVERT: F 113 ARG cc_start: 0.8051 (ptt-90) cc_final: 0.7847 (ptp-170) REVERT: F 118 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8241 (tmmm) REVERT: G 49 GLN cc_start: 0.8521 (mm110) cc_final: 0.8285 (mm110) REVERT: G 55 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: G 97 LYS cc_start: 0.8312 (tppt) cc_final: 0.7985 (mptt) REVERT: G 196 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7219 (mtp85) REVERT: G 236 ASP cc_start: 0.8579 (t0) cc_final: 0.7857 (t0) REVERT: G 260 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: G 335 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6957 (mm-30) REVERT: G 381 ASP cc_start: 0.8595 (t0) cc_final: 0.8334 (t0) REVERT: H 239 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8072 (mp10) outliers start: 66 outliers final: 44 residues processed: 198 average time/residue: 0.5465 time to fit residues: 122.6232 Evaluate side-chains 196 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 262 ARG 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 445 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE 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 208 TRP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL 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 118 LYS Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 VAL 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 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 Chi-restraints excluded: chain H residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 156 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 82 ASN F 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.082394 restraints weight = 27989.322| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.22 r_work: 0.2885 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17668 Z= 0.124 Angle : 0.546 9.015 23990 Z= 0.273 Chirality : 0.042 0.315 2733 Planarity : 0.004 0.042 2929 Dihedral : 9.288 179.847 2471 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.33 % Rotamer: Outliers : 3.35 % Allowed : 24.01 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 2045 helix: 2.24 (0.17), residues: 868 sheet: -0.23 (0.28), residues: 383 loop : -1.48 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 74 TYR 0.015 0.001 TYR E 114 PHE 0.016 0.001 PHE A 370 TRP 0.010 0.001 TRP A 538 HIS 0.003 0.001 HIS H 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (17643) covalent geometry : angle 0.53805 / 0.27 (23918) hydrogen bonds : bond 0.04201 / 2.80 ( 765) hydrogen bonds : angle 3.89594 / 2.80 ( 2220) Misc. bond : bond 0.00036 / 0.02 ( 1) link_ALPHA1-2 : bond 0.00188 / 0.11 ( 5) link_ALPHA1-2 : angle 1.65715 / 0.98 ( 15) link_ALPHA1-3 : bond 0.00671 / 0.40 ( 5) link_ALPHA1-3 : angle 1.23154 / 0.83 ( 15) link_ALPHA1-6 : bond 0.00590 / 0.28 ( 2) link_ALPHA1-6 : angle 1.72816 / 0.94 ( 6) link_BETA1-4 : bond 0.00308 / 0.17 ( 7) link_BETA1-4 : angle 1.57199 / 0.96 ( 21) link_NAG-ASN : bond 0.00330 / 0.19 ( 5) link_NAG-ASN : angle 2.37999 / 1.54 ( 15) *********************** 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 212 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8641 (m) REVERT: A 262 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7779 (mtm110) REVERT: A 352 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: B 1 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7658 (ttt) REVERT: D 69 ARG cc_start: 0.7516 (mmm160) cc_final: 0.6398 (tpp-160) REVERT: E 243 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.8998 (p) REVERT: E 266 LYS cc_start: 0.7883 (mmtm) cc_final: 0.7580 (pptt) REVERT: E 393 ASP cc_start: 0.8611 (m-30) cc_final: 0.8333 (m-30) REVERT: F 113 ARG cc_start: 0.8014 (ptt-90) cc_final: 0.7644 (ptp-170) REVERT: F 118 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8260 (tmmm) REVERT: F 125 GLN cc_start: 0.8116 (mt0) cc_final: 0.7875 (pt0) REVERT: G 49 GLN cc_start: 0.8478 (mm110) cc_final: 0.8270 (mm110) REVERT: G 55 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: G 97 LYS cc_start: 0.8302 (tppt) cc_final: 0.7978 (mptt) REVERT: G 196 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7209 (mtp85) REVERT: G 236 ASP cc_start: 0.8576 (t0) cc_final: 0.7853 (t0) REVERT: G 260 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: G 335 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6975 (mm-30) REVERT: G 381 ASP cc_start: 0.8595 (t0) cc_final: 0.8320 (t0) REVERT: H 239 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8062 (mp10) outliers start: 60 outliers final: 41 residues processed: 198 average time/residue: 0.5530 time to fit residues: 124.2974 Evaluate side-chains 194 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 145 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 262 ARG 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 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 545 ILE Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 58 ILE 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 243 SER Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL 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 118 LYS Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 VAL 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 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 Chi-restraints excluded: chain H residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.206 > 50: distance: 16 - 22: 25.391 distance: 17 - 48: 23.215 distance: 22 - 23: 30.168 distance: 23 - 24: 54.919 distance: 23 - 26: 44.072 distance: 24 - 25: 45.652 distance: 24 - 33: 32.893 distance: 26 - 27: 47.852 distance: 27 - 28: 25.078 distance: 27 - 29: 44.596 distance: 28 - 30: 14.896 distance: 29 - 31: 40.233 distance: 30 - 32: 43.538 distance: 31 - 32: 51.890 distance: 33 - 34: 41.294 distance: 34 - 35: 56.163 distance: 34 - 37: 54.011 distance: 35 - 36: 46.108 distance: 35 - 41: 55.477 distance: 36 - 73: 13.520 distance: 37 - 38: 42.417 distance: 38 - 39: 20.895 distance: 38 - 40: 31.481 distance: 41 - 42: 37.573 distance: 41 - 47: 11.219 distance: 42 - 43: 36.070 distance: 42 - 45: 40.340 distance: 43 - 44: 20.278 distance: 43 - 48: 53.757 distance: 44 - 81: 45.143 distance: 46 - 47: 10.868 distance: 48 - 49: 56.526 distance: 49 - 50: 48.375 distance: 49 - 52: 62.963 distance: 50 - 51: 43.285 distance: 50 - 62: 46.139 distance: 51 - 93: 9.074 distance: 52 - 53: 54.908 distance: 53 - 54: 36.995 distance: 53 - 55: 26.312 distance: 54 - 56: 19.650 distance: 55 - 57: 24.018 distance: 55 - 58: 10.449 distance: 56 - 57: 28.905 distance: 57 - 59: 17.836 distance: 58 - 60: 10.300 distance: 59 - 61: 14.998 distance: 60 - 61: 12.108 distance: 62 - 63: 41.383 distance: 63 - 64: 44.586 distance: 63 - 66: 38.412 distance: 64 - 65: 28.802 distance: 64 - 73: 46.104 distance: 65 - 104: 35.288 distance: 66 - 67: 18.896 distance: 67 - 68: 46.510 distance: 67 - 69: 34.431 distance: 68 - 70: 46.857 distance: 69 - 71: 31.078 distance: 70 - 72: 19.314 distance: 71 - 72: 23.628 distance: 73 - 74: 65.046 distance: 74 - 75: 66.950 distance: 74 - 77: 45.849 distance: 75 - 76: 44.816 distance: 75 - 81: 67.206 distance: 76 - 109: 32.824 distance: 77 - 78: 32.089 distance: 78 - 79: 41.029 distance: 78 - 80: 41.537 distance: 81 - 82: 51.496 distance: 82 - 83: 28.674 distance: 82 - 85: 34.829 distance: 83 - 84: 20.849 distance: 83 - 93: 32.692 distance: 84 - 116: 22.976 distance: 85 - 86: 39.349 distance: 86 - 87: 33.987 distance: 86 - 88: 20.550 distance: 87 - 89: 24.281 distance: 88 - 90: 31.391 distance: 89 - 91: 8.691 distance: 90 - 91: 15.405 distance: 91 - 92: 6.816 distance: 93 - 94: 47.994 distance: 94 - 95: 43.411 distance: 94 - 97: 43.384 distance: 95 - 96: 32.013 distance: 95 - 104: 41.733 distance: 96 - 125: 26.986 distance: 97 - 98: 31.349 distance: 98 - 99: 37.234 distance: 99 - 100: 34.720 distance: 100 - 101: 26.192 distance: 101 - 102: 33.693 distance: 101 - 103: 15.180 distance: 104 - 105: 33.935 distance: 105 - 106: 30.635 distance: 105 - 108: 28.034 distance: 106 - 107: 16.350 distance: 106 - 109: 11.029 distance: 107 - 132: 22.242 distance: 109 - 110: 29.704 distance: 110 - 111: 27.147 distance: 110 - 113: 11.052 distance: 111 - 112: 11.062 distance: 111 - 116: 23.195 distance: 112 - 139: 20.017 distance: 113 - 114: 4.980 distance: 113 - 115: 24.506