Starting phenix.real_space_refine on Sat Aug 8 04:41:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9td2_55800/08_2026/9td2_55800_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9td2_55800/08_2026/9td2_55800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9td2_55800/08_2026/9td2_55800_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9td2_55800/08_2026/9td2_55800_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9td2_55800/08_2026/9td2_55800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9td2_55800/08_2026/9td2_55800.map" } resolution = 2.64 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= 0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 6 9.91 5 Mg 1 5.21 5 S 87 5.16 5 C 7950 2.51 5 N 2173 2.21 5 O 2549 1.98 5 H 12054 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24820 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 9008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 9008 Classifications: {'peptide': 599} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 37, 'TRANS': 561} Chain: "B" Number of atoms: 8821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 8821 Classifications: {'peptide': 592} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 562} Chain breaks: 2 Chain: "H" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3525 Classifications: {'peptide': 238} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 222} Chain: "L" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3238 Classifications: {'peptide': 214} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' CA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.24, per 1000 atoms: 0.13 Number of scatterers: 24820 At special positions: 0 Unit cell: (87.6973, 109.364, 202.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 6 19.99 S 87 16.00 Mg 1 11.99 O 2549 8.00 N 2173 7.00 C 7950 6.00 H 12054 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.04 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.04 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.04 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.02 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.02 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 238 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " MAN F 3 " - " MAN F 4 " ALPHA1-4 " NAG F 2 " - " MAN F 3 " " NAG G 2 " - " MAN G 3 " " NAG J 2 " - " MAN J 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1005 " - " ASN A 15 " " NAG A1006 " - " ASN A 570 " " NAG E 1 " - " ASN B 99 " " NAG F 1 " - " ASN B 320 " " NAG G 1 " - " ASN B 371 " " NAG I 1 " - " ASN B 559 " " NAG J 1 " - " ASN B 452 " Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 565.2 milliseconds 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 35 sheets defined 13.5% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.629A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 515 through 519 removed outlier: 4.102A pdb=" N ARG A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.733A pdb=" N PHE A 558 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.075A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.818A pdb=" N LYS B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 175 removed outlier: 3.673A pdb=" N LEU B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 removed outlier: 4.031A pdb=" N PHE B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 removed outlier: 3.614A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 258 through 264 removed outlier: 3.740A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.192A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 314 through 325 removed outlier: 3.633A pdb=" N LEU B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 493 through 497 removed outlier: 4.153A pdb=" N SER B 496 " --> pdb=" O PRO B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 538 Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 149 through 151 No H-bonds generated for 'chain 'H' and resid 149 through 151' Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 7.150A pdb=" N PHE A 10 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL A 425 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE A 436 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY A 423 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLY A 438 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 421 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.597A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.553A pdb=" N SER A 172 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.472A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.556A pdb=" N LEU A 345 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.696A pdb=" N GLU A 315 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 323 " --> pdb=" O GLU A 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.861A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.752A pdb=" N CYS A 473 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER A 483 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.752A pdb=" N CYS A 473 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.581A pdb=" N VAL A 592 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB6, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.539A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 386 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.985A pdb=" N SER B 396 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 373 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 190 through 197 removed outlier: 7.167A pdb=" N VAL B 193 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA B 155 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 112 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N GLY B 152 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 114 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY B 154 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B 116 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE B 156 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET B 118 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP B 113 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL B 247 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B 115 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR B 249 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU B 117 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 453 through 456 Processing sheet with id=AC1, first strand: chain 'B' and resid 466 through 467 Processing sheet with id=AC2, first strand: chain 'B' and resid 499 through 501 removed outlier: 3.504A pdb=" N GLU B 500 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 540 through 543 Processing sheet with id=AC4, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.522A pdb=" N CYS B 560 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 580 through 582 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.518A pdb=" N LEU H 20 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.518A pdb=" N LEU H 20 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.570A pdb=" N VAL H 12 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA H 34 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE H 55 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER H 42 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU H 47 " --> pdb=" O SER H 42 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.570A pdb=" N VAL H 12 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 124 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 142 through 146 removed outlier: 5.984A pdb=" N TYR H 198 " --> pdb=" O ASP H 166 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 153 through 154 removed outlier: 5.984A pdb=" N TYR H 198 " --> pdb=" O ASP H 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 173 through 176 removed outlier: 4.513A pdb=" N TYR H 216 " --> pdb=" O VAL H 233 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.763A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.287A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.050A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.375A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12054 1.03 - 1.23: 174 1.23 - 1.43: 5362 1.43 - 1.63: 7385 1.63 - 1.82: 108 Bond restraints: 25083 Sorted by residual: bond pdb=" CD1 TYR A 288 " pdb=" CE1 TYR A 288 " ideal model delta sigma weight residual 1.382 1.322 0.060 3.00e-02 1.11e+03 3.96e+00 bond pdb=" CB TYR A 288 " pdb=" CG TYR A 288 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.20e-02 2.07e+03 2.80e+00 bond pdb=" CG LEU L 46 " pdb=" CD1 LEU L 46 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CG LEU A 322 " pdb=" CD1 LEU A 322 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.61e+00 bond pdb=" C1 NAG F 2 " pdb=" C2 NAG F 2 " ideal model delta sigma weight residual 1.532 1.502 0.030 2.00e-02 2.50e+03 2.32e+00 ... (remaining 25078 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 44368 1.74 - 3.49: 662 3.49 - 5.23: 89 5.23 - 6.98: 19 6.98 - 8.72: 3 Bond angle restraints: 45141 Sorted by residual: angle pdb=" C ASN B 376 " pdb=" CA ASN B 376 " pdb=" CB ASN B 376 " ideal model delta sigma weight residual 116.63 111.13 5.50 1.16e+00 7.43e-01 2.25e+01 angle pdb=" CA TYR A 166 " pdb=" CB TYR A 166 " pdb=" CG TYR A 166 " ideal model delta sigma weight residual 113.90 107.02 6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C ILE B 256 " pdb=" CA ILE B 256 " pdb=" CB ILE B 256 " ideal model delta sigma weight residual 111.29 117.23 -5.94 1.64e+00 3.72e-01 1.31e+01 angle pdb=" N LYS A 321 " pdb=" CA LYS A 321 " pdb=" C LYS A 321 " ideal model delta sigma weight residual 111.14 114.98 -3.84 1.08e+00 8.57e-01 1.26e+01 angle pdb=" CB ARG A 597 " pdb=" CG ARG A 597 " pdb=" CD ARG A 597 " ideal model delta sigma weight residual 111.30 119.07 -7.77 2.30e+00 1.89e-01 1.14e+01 ... (remaining 45136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 11610 23.02 - 46.04: 486 46.04 - 69.07: 129 69.07 - 92.09: 26 92.09 - 115.11: 3 Dihedral angle restraints: 12254 sinusoidal: 6837 harmonic: 5417 Sorted by residual: dihedral pdb=" CB CYS B 495 " pdb=" SG CYS B 495 " pdb=" SG CYS B 506 " pdb=" CB CYS B 506 " ideal model delta sinusoidal sigma weight residual 93.00 -179.80 -87.20 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A 473 " pdb=" SG CYS A 473 " pdb=" SG CYS A 484 " pdb=" CB CYS A 484 " ideal model delta sinusoidal sigma weight residual -86.00 -147.46 61.46 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS B 536 " pdb=" SG CYS B 536 " pdb=" SG CYS B 547 " pdb=" CB CYS B 547 " ideal model delta sinusoidal sigma weight residual 93.00 136.73 -43.73 1 1.00e+01 1.00e-02 2.66e+01 ... (remaining 12251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 1999 0.219 - 0.438: 1 0.438 - 0.657: 0 0.657 - 0.876: 0 0.876 - 1.095: 1 Chirality restraints: 2001 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 452 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-01 2.50e+01 3.00e+01 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 371 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.31e+00 ... (remaining 1998 not shown) Planarity restraints: 3851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 371 " -0.000 2.00e-02 2.50e+03 3.21e-02 1.29e+01 pdb=" CG ASN B 371 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 371 " 0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN B 371 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 99 " 0.024 2.00e-02 2.50e+03 2.16e-02 5.83e+00 pdb=" CG ASN B 99 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 99 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 99 " -0.019 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 257 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C ALA B 257 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 257 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 258 " -0.012 2.00e-02 2.50e+03 ... (remaining 3848 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.24: 2939 2.24 - 2.83: 55257 2.83 - 3.42: 62592 3.42 - 4.01: 91174 4.01 - 4.60: 135694 Nonbonded interactions: 347656 Sorted by model distance: nonbonded pdb=" OD1 ASP A 369 " pdb=" O HOH A1101 " model vdw 1.655 2.800 nonbonded pdb=" O TYR A 371 " pdb=" O HOH A1101 " model vdw 1.719 2.800 nonbonded pdb=" HD2 TYR A 288 " pdb=" HB2 HIS A 291 " model vdw 1.783 2.270 nonbonded pdb=" H VAL A 325 " pdb=" H GLY A 326 " model vdw 1.807 2.100 nonbonded pdb=" HD2 HIS H 116 " pdb=" H TYR H 118 " model vdw 1.818 2.100 ... (remaining 347651 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' } 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.340 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.004 0.064 13078 Z= 0.198 Angle : 0.803 18.883 17819 Z= 0.400 Chirality : 0.053 1.095 2001 Planarity : 0.005 0.047 2300 Dihedral : 12.478 115.109 4991 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -1.58 (0.19), residues: 1631 helix: -2.10 (0.32), residues: 138 sheet: -0.54 (0.21), residues: 562 loop : -1.17 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 216 TYR 0.029 0.002 TYR A 166 PHE 0.014 0.002 PHE A 289 TRP 0.013 0.002 TRP A 235 HIS 0.009 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (13029) covalent geometry : angle 0.71006 / 0.38 (17705) SS BOND : bond 0.00396 / 0.25 ( 33) SS BOND : angle 1.34633 / 0.95 ( 66) hydrogen bonds : bond 0.17822 / 12.02 ( 425) hydrogen bonds : angle 8.37567 / 5.70 ( 1155) link_ALPHA1-3 : bond 0.00727 / 0.35 ( 1) link_ALPHA1-3 : angle 6.80080 / 3.40 ( 3) link_ALPHA1-4 : bond 0.01850 / 0.89 ( 3) link_ALPHA1-4 : angle 9.73803 / 4.36 ( 9) link_BETA1-4 : bond 0.00859 / 0.47 ( 5) link_BETA1-4 : angle 4.80231 / 2.33 ( 15) link_NAG-ASN : bond 0.01029 / 0.53 ( 7) link_NAG-ASN : angle 7.29915 / 5.04 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 LEU cc_start: 0.8855 (mt) cc_final: 0.8580 (tt) REVERT: B 568 MET cc_start: 0.6304 (tpp) cc_final: 0.6065 (tpp) REVERT: L 152 ASN cc_start: 0.8365 (t0) cc_final: 0.7856 (t0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 1.1234 time to fit residues: 222.8489 Evaluate side-chains 93 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.114652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.086188 restraints weight = 112630.444| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.88 r_work: 0.3698 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13078 Z= 0.197 Angle : 0.664 13.395 17819 Z= 0.324 Chirality : 0.046 0.632 2001 Planarity : 0.005 0.043 2300 Dihedral : 8.545 101.499 2100 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.81 % Rotamer: Outliers : 0.86 % Allowed : 7.30 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -1.05 (0.20), residues: 1631 helix: -1.00 (0.38), residues: 146 sheet: -0.38 (0.21), residues: 570 loop : -0.79 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.013 0.001 TYR A 166 PHE 0.011 0.001 PHE A 289 TRP 0.009 0.001 TRP A 235 HIS 0.009 0.001 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (13029) covalent geometry : angle 0.62476 / 0.32 (17705) SS BOND : bond 0.00384 / 0.24 ( 33) SS BOND : angle 1.09839 / 0.81 ( 66) hydrogen bonds : bond 0.03988 / 2.70 ( 425) hydrogen bonds : angle 6.80289 / 4.61 ( 1155) link_ALPHA1-3 : bond 0.01400 / 0.67 ( 1) link_ALPHA1-3 : angle 2.03718 / 0.77 ( 3) link_ALPHA1-4 : bond 0.01921 / 0.92 ( 3) link_ALPHA1-4 : angle 4.94095 / 2.06 ( 9) link_BETA1-4 : bond 0.00482 / 0.24 ( 5) link_BETA1-4 : angle 2.87252 / 1.55 ( 15) link_NAG-ASN : bond 0.00903 / 0.47 ( 7) link_NAG-ASN : angle 4.91157 / 3.56 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 LEU cc_start: 0.9008 (mt) cc_final: 0.8766 (tt) REVERT: B 171 GLU cc_start: 0.7451 (mp0) cc_final: 0.7090 (mp0) REVERT: B 335 MET cc_start: 0.7291 (pmm) cc_final: 0.6982 (tpt) REVERT: B 539 HIS cc_start: 0.7830 (m170) cc_final: 0.7035 (m170) REVERT: L 152 ASN cc_start: 0.8904 (t0) cc_final: 0.8534 (t0) outliers start: 12 outliers final: 5 residues processed: 103 average time/residue: 0.9056 time to fit residues: 104.4406 Evaluate side-chains 88 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 135 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.112505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.084153 restraints weight = 112572.681| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.73 r_work: 0.3654 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13078 Z= 0.213 Angle : 0.641 12.263 17819 Z= 0.314 Chirality : 0.045 0.587 2001 Planarity : 0.004 0.042 2300 Dihedral : 7.426 88.123 2100 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 1.22 % Allowed : 8.01 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.92 (0.20), residues: 1631 helix: -0.68 (0.42), residues: 146 sheet: -0.32 (0.21), residues: 564 loop : -0.72 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 8 TYR 0.015 0.002 TYR A 166 PHE 0.012 0.002 PHE B 203 TRP 0.022 0.002 TRP B 553 HIS 0.007 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (13029) covalent geometry : angle 0.60874 / 0.31 (17705) SS BOND : bond 0.00380 / 0.22 ( 33) SS BOND : angle 0.87376 / 0.60 ( 66) hydrogen bonds : bond 0.03629 / 2.46 ( 425) hydrogen bonds : angle 6.45407 / 4.36 ( 1155) link_ALPHA1-3 : bond 0.01029 / 0.49 ( 1) link_ALPHA1-3 : angle 1.38880 / 0.49 ( 3) link_ALPHA1-4 : bond 0.01452 / 0.70 ( 3) link_ALPHA1-4 : angle 3.99544 / 1.75 ( 9) link_BETA1-4 : bond 0.00596 / 0.30 ( 5) link_BETA1-4 : angle 2.96170 / 1.56 ( 15) link_NAG-ASN : bond 0.00787 / 0.41 ( 7) link_NAG-ASN : angle 4.53496 / 3.22 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8015 (mt) REVERT: A 142 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7209 (mp0) REVERT: B 8 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7113 (tmm-80) REVERT: B 118 MET cc_start: 0.6820 (tpp) cc_final: 0.6595 (tpt) REVERT: H 122 MET cc_start: 0.7629 (mtt) cc_final: 0.7239 (mtt) outliers start: 17 outliers final: 9 residues processed: 99 average time/residue: 0.9975 time to fit residues: 109.6720 Evaluate side-chains 90 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 355 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.112418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.084097 restraints weight = 112470.466| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.73 r_work: 0.3655 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13078 Z= 0.151 Angle : 0.591 11.527 17819 Z= 0.286 Chirality : 0.044 0.576 2001 Planarity : 0.004 0.043 2300 Dihedral : 6.932 83.501 2100 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 0.93 % Allowed : 9.08 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.75 (0.21), residues: 1631 helix: -0.42 (0.43), residues: 146 sheet: -0.26 (0.21), residues: 565 loop : -0.59 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 56 TYR 0.012 0.001 TYR A 166 PHE 0.009 0.001 PHE A 191 TRP 0.008 0.001 TRP A 58 HIS 0.005 0.001 HIS H 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (13029) covalent geometry : angle 0.56207 / 0.28 (17705) SS BOND : bond 0.00369 / 0.20 ( 33) SS BOND : angle 0.78213 / 0.57 ( 66) hydrogen bonds : bond 0.03089 / 2.11 ( 425) hydrogen bonds : angle 6.23160 / 4.21 ( 1155) link_ALPHA1-3 : bond 0.00818 / 0.39 ( 1) link_ALPHA1-3 : angle 1.53718 / 0.52 ( 3) link_ALPHA1-4 : bond 0.01284 / 0.63 ( 3) link_ALPHA1-4 : angle 3.52245 / 1.49 ( 9) link_BETA1-4 : bond 0.00527 / 0.26 ( 5) link_BETA1-4 : angle 2.48763 / 1.32 ( 15) link_NAG-ASN : bond 0.00787 / 0.41 ( 7) link_NAG-ASN : angle 4.23997 / 3.05 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 MET cc_start: 0.6933 (mmt) cc_final: 0.6687 (mpp) REVERT: B 124 MET cc_start: 0.7627 (mmt) cc_final: 0.7069 (mmt) REVERT: H 122 MET cc_start: 0.7651 (mtt) cc_final: 0.7325 (mtt) outliers start: 13 outliers final: 8 residues processed: 85 average time/residue: 1.0789 time to fit residues: 101.1553 Evaluate side-chains 84 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.112435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.084151 restraints weight = 111811.339| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.76 r_work: 0.3662 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13078 Z= 0.136 Angle : 0.569 11.061 17819 Z= 0.275 Chirality : 0.044 0.550 2001 Planarity : 0.004 0.041 2300 Dihedral : 6.487 78.487 2100 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 0.72 % Allowed : 10.23 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.69 (0.21), residues: 1631 helix: -0.27 (0.43), residues: 146 sheet: -0.25 (0.22), residues: 572 loop : -0.54 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 56 TYR 0.015 0.001 TYR A 288 PHE 0.010 0.001 PHE A 191 TRP 0.008 0.001 TRP A 58 HIS 0.004 0.001 HIS H 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13029) covalent geometry : angle 0.54238 / 0.27 (17705) SS BOND : bond 0.00283 / 0.16 ( 33) SS BOND : angle 0.69256 / 0.50 ( 66) hydrogen bonds : bond 0.02923 / 2.00 ( 425) hydrogen bonds : angle 6.08089 / 4.11 ( 1155) link_ALPHA1-3 : bond 0.01219 / 0.58 ( 1) link_ALPHA1-3 : angle 1.76783 / 0.59 ( 3) link_ALPHA1-4 : bond 0.01366 / 0.67 ( 3) link_ALPHA1-4 : angle 3.32873 / 1.43 ( 9) link_BETA1-4 : bond 0.00395 / 0.20 ( 5) link_BETA1-4 : angle 2.18957 / 1.18 ( 15) link_NAG-ASN : bond 0.00741 / 0.39 ( 7) link_NAG-ASN : angle 4.05739 / 2.92 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8309 (mp) cc_final: 0.7939 (mt) REVERT: B 124 MET cc_start: 0.7677 (mmt) cc_final: 0.7050 (mmt) REVERT: H 122 MET cc_start: 0.7716 (mtt) cc_final: 0.7367 (mtt) REVERT: L 107 ILE cc_start: 0.9200 (mp) cc_final: 0.8699 (tp) outliers start: 10 outliers final: 6 residues processed: 82 average time/residue: 1.0961 time to fit residues: 99.0341 Evaluate side-chains 81 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.110517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.081913 restraints weight = 112633.599| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.71 r_work: 0.3614 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13078 Z= 0.210 Angle : 0.618 11.144 17819 Z= 0.301 Chirality : 0.044 0.539 2001 Planarity : 0.004 0.045 2300 Dihedral : 6.127 59.688 2100 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 1.14 % Allowed : 10.52 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.79 (0.21), residues: 1631 helix: -0.33 (0.43), residues: 146 sheet: -0.24 (0.22), residues: 551 loop : -0.67 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 516 TYR 0.023 0.002 TYR A 288 PHE 0.011 0.002 PHE B 203 TRP 0.010 0.001 TRP B 129 HIS 0.006 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (13029) covalent geometry : angle 0.59368 / 0.30 (17705) SS BOND : bond 0.00333 / 0.18 ( 33) SS BOND : angle 0.81066 / 0.56 ( 66) hydrogen bonds : bond 0.03139 / 2.13 ( 425) hydrogen bonds : angle 6.08047 / 4.12 ( 1155) link_ALPHA1-3 : bond 0.00852 / 0.41 ( 1) link_ALPHA1-3 : angle 1.67870 / 0.52 ( 3) link_ALPHA1-4 : bond 0.01204 / 0.60 ( 3) link_ALPHA1-4 : angle 3.07023 / 1.41 ( 9) link_BETA1-4 : bond 0.00345 / 0.17 ( 5) link_BETA1-4 : angle 2.11919 / 1.17 ( 15) link_NAG-ASN : bond 0.00745 / 0.38 ( 7) link_NAG-ASN : angle 4.20394 / 2.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8419 (mp) cc_final: 0.8020 (mt) REVERT: B 124 MET cc_start: 0.7705 (mmt) cc_final: 0.7124 (mmt) REVERT: L 107 ILE cc_start: 0.9202 (mp) cc_final: 0.8751 (tp) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 1.0378 time to fit residues: 103.3207 Evaluate side-chains 84 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 135 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 120 optimal weight: 0.0060 chunk 134 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.111370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.082950 restraints weight = 112161.506| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.78 r_work: 0.3622 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13078 Z= 0.129 Angle : 0.570 10.618 17819 Z= 0.275 Chirality : 0.044 0.532 2001 Planarity : 0.004 0.049 2300 Dihedral : 5.571 53.140 2100 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 0.93 % Allowed : 11.16 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.68 (0.21), residues: 1631 helix: -0.19 (0.44), residues: 146 sheet: -0.21 (0.22), residues: 548 loop : -0.57 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 489 TYR 0.017 0.001 TYR A 288 PHE 0.011 0.001 PHE A 191 TRP 0.009 0.001 TRP A 58 HIS 0.004 0.001 HIS H 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13029) covalent geometry : angle 0.54775 / 0.27 (17705) SS BOND : bond 0.00237 / 0.13 ( 33) SS BOND : angle 0.61396 / 0.43 ( 66) hydrogen bonds : bond 0.02818 / 1.93 ( 425) hydrogen bonds : angle 5.89187 / 3.98 ( 1155) link_ALPHA1-3 : bond 0.00929 / 0.44 ( 1) link_ALPHA1-3 : angle 1.60214 / 0.49 ( 3) link_ALPHA1-4 : bond 0.01284 / 0.64 ( 3) link_ALPHA1-4 : angle 2.88532 / 1.32 ( 9) link_BETA1-4 : bond 0.00350 / 0.18 ( 5) link_BETA1-4 : angle 1.94946 / 1.08 ( 15) link_NAG-ASN : bond 0.00710 / 0.37 ( 7) link_NAG-ASN : angle 3.91515 / 2.82 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8337 (mp) cc_final: 0.7923 (mt) REVERT: B 124 MET cc_start: 0.7633 (mmt) cc_final: 0.7086 (mmt) REVERT: B 568 MET cc_start: 0.5580 (tpp) cc_final: 0.4477 (tpp) REVERT: L 107 ILE cc_start: 0.9199 (mp) cc_final: 0.8752 (tp) outliers start: 13 outliers final: 10 residues processed: 84 average time/residue: 1.0186 time to fit residues: 95.1892 Evaluate side-chains 82 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 59 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.110018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.081219 restraints weight = 111147.558| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.75 r_work: 0.3610 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13078 Z= 0.191 Angle : 0.588 10.728 17819 Z= 0.287 Chirality : 0.044 0.522 2001 Planarity : 0.004 0.047 2300 Dihedral : 5.459 52.900 2100 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 1.00 % Allowed : 11.02 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.77 (0.21), residues: 1631 helix: -0.23 (0.44), residues: 146 sheet: -0.28 (0.22), residues: 552 loop : -0.63 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 489 TYR 0.018 0.001 TYR A 288 PHE 0.011 0.001 PHE B 203 TRP 0.009 0.001 TRP B 129 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (13029) covalent geometry : angle 0.56413 / 0.28 (17705) SS BOND : bond 0.00286 / 0.16 ( 33) SS BOND : angle 0.71336 / 0.48 ( 66) hydrogen bonds : bond 0.02994 / 2.03 ( 425) hydrogen bonds : angle 5.92569 / 4.01 ( 1155) link_ALPHA1-3 : bond 0.01052 / 0.50 ( 1) link_ALPHA1-3 : angle 1.66566 / 0.50 ( 3) link_ALPHA1-4 : bond 0.00925 / 0.46 ( 3) link_ALPHA1-4 : angle 2.73105 / 1.32 ( 9) link_BETA1-4 : bond 0.00325 / 0.17 ( 5) link_BETA1-4 : angle 2.21063 / 1.18 ( 15) link_NAG-ASN : bond 0.00735 / 0.38 ( 7) link_NAG-ASN : angle 4.03011 / 2.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7661 (mmt) cc_final: 0.7105 (mmt) REVERT: B 568 MET cc_start: 0.5746 (tpp) cc_final: 0.4572 (tpp) REVERT: H 122 MET cc_start: 0.7646 (mtt) cc_final: 0.7404 (mtt) REVERT: L 107 ILE cc_start: 0.9205 (mp) cc_final: 0.8726 (tp) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 1.0766 time to fit residues: 99.2532 Evaluate side-chains 78 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 55 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.110842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.082073 restraints weight = 111248.425| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.80 r_work: 0.3630 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13078 Z= 0.122 Angle : 0.565 10.330 17819 Z= 0.274 Chirality : 0.044 0.515 2001 Planarity : 0.004 0.050 2300 Dihedral : 5.201 52.856 2100 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 0.57 % Allowed : 11.44 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.68 (0.21), residues: 1631 helix: -0.13 (0.44), residues: 146 sheet: -0.24 (0.22), residues: 550 loop : -0.56 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 489 TYR 0.021 0.001 TYR B 178 PHE 0.011 0.001 PHE A 191 TRP 0.009 0.001 TRP A 58 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13029) covalent geometry : angle 0.54202 / 0.27 (17705) SS BOND : bond 0.00211 / 0.12 ( 33) SS BOND : angle 0.89772 / 0.56 ( 66) hydrogen bonds : bond 0.02698 / 1.84 ( 425) hydrogen bonds : angle 5.77160 / 3.90 ( 1155) link_ALPHA1-3 : bond 0.01169 / 0.56 ( 1) link_ALPHA1-3 : angle 1.63186 / 0.51 ( 3) link_ALPHA1-4 : bond 0.00818 / 0.40 ( 3) link_ALPHA1-4 : angle 2.61567 / 1.25 ( 9) link_BETA1-4 : bond 0.00382 / 0.20 ( 5) link_BETA1-4 : angle 2.07711 / 1.10 ( 15) link_NAG-ASN : bond 0.00709 / 0.37 ( 7) link_NAG-ASN : angle 3.79316 / 2.74 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7647 (mmt) cc_final: 0.7105 (mmt) REVERT: B 568 MET cc_start: 0.5538 (tpp) cc_final: 0.4517 (tpp) REVERT: H 122 MET cc_start: 0.7557 (mtt) cc_final: 0.7245 (mtt) REVERT: L 107 ILE cc_start: 0.9197 (mp) cc_final: 0.8721 (tp) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 1.0900 time to fit residues: 94.7609 Evaluate side-chains 75 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.110116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.081654 restraints weight = 111862.575| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.75 r_work: 0.3611 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13078 Z= 0.167 Angle : 0.582 10.382 17819 Z= 0.284 Chirality : 0.044 0.510 2001 Planarity : 0.004 0.047 2300 Dihedral : 5.177 53.109 2100 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.57 % Allowed : 11.37 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.77 (0.21), residues: 1631 helix: -0.17 (0.44), residues: 146 sheet: -0.32 (0.22), residues: 559 loop : -0.62 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 489 TYR 0.018 0.001 TYR A 288 PHE 0.010 0.001 PHE B 203 TRP 0.009 0.001 TRP B 129 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (13029) covalent geometry : angle 0.55890 / 0.28 (17705) SS BOND : bond 0.00256 / 0.14 ( 33) SS BOND : angle 0.85386 / 0.54 ( 66) hydrogen bonds : bond 0.02848 / 1.93 ( 425) hydrogen bonds : angle 5.79838 / 3.92 ( 1155) link_ALPHA1-3 : bond 0.01089 / 0.52 ( 1) link_ALPHA1-3 : angle 1.60214 / 0.50 ( 3) link_ALPHA1-4 : bond 0.00600 / 0.29 ( 3) link_ALPHA1-4 : angle 2.40824 / 1.18 ( 9) link_BETA1-4 : bond 0.00327 / 0.17 ( 5) link_BETA1-4 : angle 2.10258 / 1.11 ( 15) link_NAG-ASN : bond 0.00718 / 0.37 ( 7) link_NAG-ASN : angle 3.91203 / 2.77 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3262 Ramachandran restraints generated. 1631 Oldfield, 0 Emsley, 1631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 250 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 MET cc_start: 0.7654 (mmt) cc_final: 0.7106 (mmt) REVERT: B 178 TYR cc_start: 0.8067 (p90) cc_final: 0.7865 (p90) REVERT: B 568 MET cc_start: 0.5621 (tpp) cc_final: 0.4479 (tpp) REVERT: H 122 MET cc_start: 0.7746 (mtt) cc_final: 0.7456 (mtt) REVERT: L 107 ILE cc_start: 0.9191 (mp) cc_final: 0.8698 (tp) outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 1.0838 time to fit residues: 91.9690 Evaluate side-chains 75 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 387 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 143 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.110073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.081744 restraints weight = 111683.341| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.77 r_work: 0.3612 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13078 Z= 0.152 Angle : 0.572 10.252 17819 Z= 0.279 Chirality : 0.044 0.510 2001 Planarity : 0.004 0.046 2300 Dihedral : 5.103 52.932 2100 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 0.72 % Allowed : 11.30 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.61 % 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: -0.74 (0.21), residues: 1631 helix: -0.18 (0.44), residues: 146 sheet: -0.29 (0.22), residues: 557 loop : -0.60 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 489 TYR 0.017 0.001 TYR A 288 PHE 0.010 0.001 PHE A 191 TRP 0.010 0.001 TRP B 129 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13029) covalent geometry : angle 0.55100 / 0.27 (17705) SS BOND : bond 0.00236 / 0.13 ( 33) SS BOND : angle 0.68744 / 0.44 ( 66) hydrogen bonds : bond 0.02754 / 1.87 ( 425) hydrogen bonds : angle 5.72953 / 3.87 ( 1155) link_ALPHA1-3 : bond 0.01018 / 0.48 ( 1) link_ALPHA1-3 : angle 1.57146 / 0.49 ( 3) link_ALPHA1-4 : bond 0.00610 / 0.30 ( 3) link_ALPHA1-4 : angle 2.31562 / 1.12 ( 9) link_BETA1-4 : bond 0.00318 / 0.16 ( 5) link_BETA1-4 : angle 2.06161 / 1.09 ( 15) link_NAG-ASN : bond 0.00682 / 0.35 ( 7) link_NAG-ASN : angle 3.84105 / 2.74 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7901.35 seconds wall clock time: 134 minutes 26.18 seconds (8066.18 seconds total)