Starting phenix.real_space_refine on Sun Jul 5 05:57:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9td2_55800/07_2026/9td2_55800_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9td2_55800/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9td2_55800/07_2026/9td2_55800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9td2_55800/07_2026/9td2_55800.map" model { file = "/net/cci-nas-00/data/ceres_data/9td2_55800/07_2026/9td2_55800_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9td2_55800/07_2026/9td2_55800_trim.cif" } 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-dev-6108/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, 28 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 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, 1 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.70, per 1000 atoms: 0.15 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: 1.77 Conformation dependent library (CDL) restraints added in 467.8 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: 0.49 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: 4.90 Time building geometry restraints manager: 2.59 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: 2.130 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: 0.130 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.800 Find NCS groups from input model: 0.090 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:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- 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 : 0.442 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: 1.0886 time to fit residues: 215.1966 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 : 0.700 ------------------------------------------------------------------------------- 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 = 0.114685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.086038 restraints weight = 112644.687| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 3.90 r_work: 0.3697 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13078 Z= 0.196 Angle : 0.664 13.313 17819 Z= 0.324 Chirality : 0.047 0.633 2001 Planarity : 0.004 0.042 2300 Dihedral : 8.535 101.489 2100 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Rotamer: Outliers : 0.79 % Allowed : 7.37 % 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: -0.37 (0.21), residues: 570 loop : -0.80 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 303 TYR 0.013 0.001 TYR A 166 PHE 0.011 0.001 PHE A 191 TRP 0.009 0.001 TRP A 235 HIS 0.009 0.002 HIS B 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (13029) covalent geometry : angle 0.62472 / 0.32 (17705) SS BOND : bond 0.00642 / 0.36 ( 33) SS BOND : angle 1.05559 / 0.76 ( 66) hydrogen bonds : bond 0.04096 / 2.77 ( 425) hydrogen bonds : angle 6.81328 / 4.62 ( 1155) link_ALPHA1-3 : bond 0.01008 / 0.48 ( 1) link_ALPHA1-3 : angle 1.94805 / 0.71 ( 3) link_ALPHA1-4 : bond 0.01940 / 0.93 ( 3) link_ALPHA1-4 : angle 5.01686 / 2.08 ( 9) link_BETA1-4 : bond 0.00533 / 0.27 ( 5) link_BETA1-4 : angle 2.89825 / 1.57 ( 15) link_NAG-ASN : bond 0.00922 / 0.48 ( 7) link_NAG-ASN : angle 4.90164 / 3.55 ( 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 105 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.726 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 475 LEU cc_start: 0.9011 (mt) cc_final: 0.8767 (tt) REVERT: B 171 GLU cc_start: 0.7439 (mp0) cc_final: 0.7084 (mp0) REVERT: B 539 HIS cc_start: 0.7817 (m170) cc_final: 0.7025 (m170) REVERT: L 152 ASN cc_start: 0.8877 (t0) cc_final: 0.8498 (t0) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 1.1248 time to fit residues: 126.3391 Evaluate side-chains 86 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.113143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.084826 restraints weight = 112302.142| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.80 r_work: 0.3667 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13078 Z= 0.188 Angle : 0.624 12.169 17819 Z= 0.304 Chirality : 0.045 0.593 2001 Planarity : 0.004 0.043 2300 Dihedral : 7.409 89.685 2100 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 1.22 % Allowed : 7.51 % Favored : 91.27 % 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: -0.90 (0.20), residues: 1631 helix: -0.67 (0.41), residues: 146 sheet: -0.30 (0.21), residues: 564 loop : -0.71 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 8 TYR 0.015 0.001 TYR A 166 PHE 0.010 0.001 PHE A 191 TRP 0.018 0.001 TRP B 553 HIS 0.006 0.001 HIS H 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (13029) covalent geometry : angle 0.59188 / 0.30 (17705) SS BOND : bond 0.00348 / 0.21 ( 33) SS BOND : angle 0.79460 / 0.55 ( 66) hydrogen bonds : bond 0.03575 / 2.42 ( 425) hydrogen bonds : angle 6.43923 / 4.35 ( 1155) link_ALPHA1-3 : bond 0.01350 / 0.64 ( 1) link_ALPHA1-3 : angle 1.54199 / 0.56 ( 3) link_ALPHA1-4 : bond 0.01824 / 0.88 ( 3) link_ALPHA1-4 : angle 3.98337 / 1.76 ( 9) link_BETA1-4 : bond 0.00651 / 0.32 ( 5) link_BETA1-4 : angle 2.85095 / 1.49 ( 15) link_NAG-ASN : bond 0.00774 / 0.40 ( 7) link_NAG-ASN : angle 4.48712 / 3.20 ( 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 102 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.842 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 142 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7103 (mp0) REVERT: B 8 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6940 (tmm-80) REVERT: B 180 MET cc_start: 0.8656 (mmm) cc_final: 0.8392 (mpm) REVERT: H 122 MET cc_start: 0.7628 (mtt) cc_final: 0.7243 (mtt) outliers start: 17 outliers final: 6 residues processed: 97 average time/residue: 1.1489 time to fit residues: 124.1444 Evaluate side-chains 86 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR 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 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: 1.9990 chunk 22 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 152 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.111270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.082882 restraints weight = 112324.297| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.70 r_work: 0.3633 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13078 Z= 0.227 Angle : 0.630 11.861 17819 Z= 0.308 Chirality : 0.045 0.574 2001 Planarity : 0.004 0.043 2300 Dihedral : 7.032 82.097 2100 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 1.22 % Allowed : 8.80 % 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: -0.95 (0.21), residues: 1631 helix: -0.59 (0.42), residues: 146 sheet: -0.38 (0.21), residues: 575 loop : -0.74 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 56 TYR 0.013 0.002 TYR A 237 PHE 0.011 0.002 PHE A 191 TRP 0.009 0.001 TRP A 58 HIS 0.006 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.23 (13029) covalent geometry : angle 0.59994 / 0.30 (17705) SS BOND : bond 0.00338 / 0.19 ( 33) SS BOND : angle 1.00626 / 0.74 ( 66) hydrogen bonds : bond 0.03382 / 2.29 ( 425) hydrogen bonds : angle 6.32704 / 4.27 ( 1155) link_ALPHA1-3 : bond 0.00707 / 0.34 ( 1) link_ALPHA1-3 : angle 1.52776 / 0.50 ( 3) link_ALPHA1-4 : bond 0.01234 / 0.60 ( 3) link_ALPHA1-4 : angle 3.50525 / 1.52 ( 9) link_BETA1-4 : bond 0.00494 / 0.25 ( 5) link_BETA1-4 : angle 2.62207 / 1.39 ( 15) link_NAG-ASN : bond 0.00794 / 0.41 ( 7) link_NAG-ASN : angle 4.43937 / 3.15 ( 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 100 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.724 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: 0.8372 (mp) cc_final: 0.8010 (mt) REVERT: A 580 MET cc_start: 0.6906 (mmt) cc_final: 0.6697 (mpp) REVERT: B 8 ARG cc_start: 0.7460 (tmm-80) cc_final: 0.7244 (tmm-80) REVERT: B 124 MET cc_start: 0.7658 (mmt) cc_final: 0.7121 (mmt) REVERT: H 122 MET cc_start: 0.7757 (mtt) cc_final: 0.7501 (mtt) outliers start: 17 outliers final: 11 residues processed: 93 average time/residue: 1.1151 time to fit residues: 114.4493 Evaluate side-chains 86 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 24 ASP 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 B residue 53 SER Chi-restraints excluded: chain B residue 127 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.111754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.083358 restraints weight = 112016.591| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.73 r_work: 0.3646 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3003 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 : 0.584 11.176 17819 Z= 0.283 Chirality : 0.044 0.558 2001 Planarity : 0.004 0.042 2300 Dihedral : 6.522 74.469 2100 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 0.79 % Allowed : 10.23 % Favored : 88.98 % 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: -0.83 (0.21), residues: 1631 helix: -0.39 (0.43), residues: 146 sheet: -0.29 (0.22), residues: 561 loop : -0.68 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 56 TYR 0.014 0.001 TYR B 178 PHE 0.010 0.001 PHE A 191 TRP 0.009 0.001 TRP A 58 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (13029) covalent geometry : angle 0.55749 / 0.28 (17705) SS BOND : bond 0.00317 / 0.18 ( 33) SS BOND : angle 0.76087 / 0.55 ( 66) hydrogen bonds : bond 0.03014 / 2.06 ( 425) hydrogen bonds : angle 6.14586 / 4.15 ( 1155) link_ALPHA1-3 : bond 0.00716 / 0.34 ( 1) link_ALPHA1-3 : angle 1.53451 / 0.50 ( 3) link_ALPHA1-4 : bond 0.01184 / 0.58 ( 3) link_ALPHA1-4 : angle 3.33208 / 1.44 ( 9) link_BETA1-4 : bond 0.00398 / 0.20 ( 5) link_BETA1-4 : angle 2.17428 / 1.18 ( 15) link_NAG-ASN : bond 0.00747 / 0.39 ( 7) link_NAG-ASN : angle 4.12376 / 2.96 ( 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 90 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.714 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: A 8 LEU cc_start: 0.8357 (mp) cc_final: 0.7961 (mt) REVERT: B 124 MET cc_start: 0.7630 (mmt) cc_final: 0.7106 (mmt) REVERT: H 122 MET cc_start: 0.7752 (mtt) cc_final: 0.7475 (mtt) REVERT: L 107 ILE cc_start: 0.9210 (mp) cc_final: 0.8713 (tp) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 1.1559 time to fit residues: 108.6542 Evaluate side-chains 81 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.109157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.080206 restraints weight = 111666.235| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.74 r_work: 0.3601 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3289 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= 0.202 Angle : 0.608 11.155 17819 Z= 0.296 Chirality : 0.044 0.543 2001 Planarity : 0.004 0.053 2300 Dihedral : 6.216 60.170 2100 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 1.29 % Allowed : 10.44 % Favored : 88.27 % 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: -0.85 (0.21), residues: 1631 helix: -0.33 (0.43), residues: 146 sheet: -0.26 (0.22), residues: 551 loop : -0.74 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 489 TYR 0.016 0.001 TYR B 178 PHE 0.013 0.001 PHE B 203 TRP 0.009 0.001 TRP A 58 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (13029) covalent geometry : angle 0.58339 / 0.29 (17705) SS BOND : bond 0.00312 / 0.17 ( 33) SS BOND : angle 0.74914 / 0.52 ( 66) hydrogen bonds : bond 0.03130 / 2.13 ( 425) hydrogen bonds : angle 6.11160 / 4.13 ( 1155) link_ALPHA1-3 : bond 0.00764 / 0.36 ( 1) link_ALPHA1-3 : angle 1.60552 / 0.49 ( 3) link_ALPHA1-4 : bond 0.01042 / 0.51 ( 3) link_ALPHA1-4 : angle 3.13425 / 1.42 ( 9) link_BETA1-4 : bond 0.00316 / 0.16 ( 5) link_BETA1-4 : angle 2.11609 / 1.16 ( 15) link_NAG-ASN : bond 0.00729 / 0.38 ( 7) link_NAG-ASN : angle 4.18418 / 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 91 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 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: A 8 LEU cc_start: 0.8413 (mp) cc_final: 0.8019 (mt) REVERT: B 8 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7200 (tmm-80) REVERT: B 124 MET cc_start: 0.7670 (mmt) cc_final: 0.7162 (mmt) REVERT: B 142 MET cc_start: 0.4485 (mmp) cc_final: 0.3949 (mmt) REVERT: L 107 ILE cc_start: 0.9223 (mp) cc_final: 0.8733 (tp) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 1.0593 time to fit residues: 101.0415 Evaluate side-chains 84 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 8 ARG Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 211 SER 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: 5.9990 chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 137 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.110039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.081174 restraints weight = 112295.091| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 3.75 r_work: 0.3636 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3388 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= 0.128 Angle : 0.571 10.627 17819 Z= 0.274 Chirality : 0.044 0.532 2001 Planarity : 0.004 0.041 2300 Dihedral : 5.599 53.289 2100 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 0.79 % Allowed : 10.94 % Favored : 88.27 % 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: -0.18 (0.44), residues: 146 sheet: -0.24 (0.22), residues: 548 loop : -0.65 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 489 TYR 0.017 0.001 TYR B 178 PHE 0.011 0.001 PHE A 191 TRP 0.009 0.001 TRP A 58 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13029) covalent geometry : angle 0.54790 / 0.27 (17705) SS BOND : bond 0.00235 / 0.13 ( 33) SS BOND : angle 0.61085 / 0.42 ( 66) hydrogen bonds : bond 0.02818 / 1.93 ( 425) hydrogen bonds : angle 5.91980 / 4.00 ( 1155) link_ALPHA1-3 : bond 0.00962 / 0.46 ( 1) link_ALPHA1-3 : angle 1.62456 / 0.50 ( 3) link_ALPHA1-4 : bond 0.01230 / 0.61 ( 3) link_ALPHA1-4 : angle 2.91125 / 1.34 ( 9) link_BETA1-4 : bond 0.00361 / 0.18 ( 5) link_BETA1-4 : angle 1.92947 / 1.06 ( 15) link_NAG-ASN : bond 0.00693 / 0.36 ( 7) link_NAG-ASN : angle 3.90723 / 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: 11 poor density : 77 time to evaluate : 0.732 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: 0.8316 (mp) cc_final: 0.7901 (mt) REVERT: B 124 MET cc_start: 0.7628 (mmt) cc_final: 0.7145 (mmt) REVERT: B 142 MET cc_start: 0.4410 (mmp) cc_final: 0.3883 (mmt) REVERT: B 568 MET cc_start: 0.5862 (tpp) cc_final: 0.5104 (tpp) REVERT: L 107 ILE cc_start: 0.9215 (mp) cc_final: 0.8729 (tp) outliers start: 11 outliers final: 7 residues processed: 85 average time/residue: 1.0781 time to fit residues: 102.7293 Evaluate side-chains 80 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR 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 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: 0.6980 chunk 106 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 139 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4341 r_free = 0.4341 target = 0.110059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.081211 restraints weight = 111475.891| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 3.80 r_work: 0.3633 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3468 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= 0.123 Angle : 0.558 10.387 17819 Z= 0.270 Chirality : 0.044 0.513 2001 Planarity : 0.004 0.041 2300 Dihedral : 5.248 53.060 2100 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 0.86 % Allowed : 10.73 % Favored : 88.41 % 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: -0.14 (0.44), residues: 146 sheet: -0.18 (0.22), residues: 544 loop : -0.62 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 489 TYR 0.019 0.001 TYR B 178 PHE 0.011 0.001 PHE A 191 TRP 0.009 0.001 TRP A 58 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13029) covalent geometry : angle 0.53597 / 0.27 (17705) SS BOND : bond 0.00222 / 0.13 ( 33) SS BOND : angle 0.59007 / 0.40 ( 66) hydrogen bonds : bond 0.02751 / 1.88 ( 425) hydrogen bonds : angle 5.79102 / 3.92 ( 1155) link_ALPHA1-3 : bond 0.01053 / 0.50 ( 1) link_ALPHA1-3 : angle 1.61676 / 0.50 ( 3) link_ALPHA1-4 : bond 0.01039 / 0.51 ( 3) link_ALPHA1-4 : angle 2.69421 / 1.29 ( 9) link_BETA1-4 : bond 0.00346 / 0.18 ( 5) link_BETA1-4 : angle 2.10294 / 1.11 ( 15) link_NAG-ASN : bond 0.00701 / 0.36 ( 7) link_NAG-ASN : angle 3.80260 / 2.74 ( 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 84 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.724 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: A 8 LEU cc_start: 0.8321 (mp) cc_final: 0.7902 (mt) REVERT: B 124 MET cc_start: 0.7609 (mmt) cc_final: 0.7152 (mmt) REVERT: H 122 MET cc_start: 0.7545 (mtt) cc_final: 0.7238 (mtt) REVERT: L 107 ILE cc_start: 0.9195 (mp) cc_final: 0.8724 (tp) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 1.1213 time to fit residues: 101.3745 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 : 0.687 ------------------------------------------------------------------------------- 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 28 ASP Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 147 SER 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: 20.0000 chunk 139 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 chunk 127 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.110939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.082460 restraints weight = 112149.323| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.82 r_work: 0.3626 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13078 Z= 0.151 Angle : 0.566 10.382 17819 Z= 0.275 Chirality : 0.044 0.512 2001 Planarity : 0.004 0.040 2300 Dihedral : 5.190 52.859 2100 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 0.79 % Allowed : 10.80 % Favored : 88.41 % 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: -0.12 (0.45), residues: 146 sheet: -0.18 (0.22), residues: 550 loop : -0.62 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 489 TYR 0.020 0.001 TYR B 178 PHE 0.010 0.001 PHE B 203 TRP 0.008 0.001 TRP A 58 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13029) covalent geometry : angle 0.54426 / 0.27 (17705) SS BOND : bond 0.00235 / 0.13 ( 33) SS BOND : angle 0.61743 / 0.42 ( 66) hydrogen bonds : bond 0.02804 / 1.91 ( 425) hydrogen bonds : angle 5.78191 / 3.91 ( 1155) link_ALPHA1-3 : bond 0.00989 / 0.47 ( 1) link_ALPHA1-3 : angle 1.57545 / 0.48 ( 3) link_ALPHA1-4 : bond 0.00819 / 0.40 ( 3) link_ALPHA1-4 : angle 2.61917 / 1.26 ( 9) link_BETA1-4 : bond 0.00328 / 0.17 ( 5) link_BETA1-4 : angle 2.11111 / 1.12 ( 15) link_NAG-ASN : bond 0.00692 / 0.36 ( 7) link_NAG-ASN : angle 3.82746 / 2.75 ( 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 82 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.723 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: A 8 LEU cc_start: 0.8338 (mp) cc_final: 0.7929 (mt) REVERT: B 124 MET cc_start: 0.7645 (mmt) cc_final: 0.7188 (mmt) REVERT: H 122 MET cc_start: 0.7581 (mtt) cc_final: 0.7312 (mtt) REVERT: L 107 ILE cc_start: 0.9197 (mp) cc_final: 0.8723 (tp) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 1.0883 time to fit residues: 97.4189 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 : 0.697 ------------------------------------------------------------------------------- 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 585 VAL Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 147 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: 0.9990 chunk 25 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 120 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.111738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.083422 restraints weight = 111387.354| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.83 r_work: 0.3648 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13078 Z= 0.105 Angle : 0.543 10.024 17819 Z= 0.264 Chirality : 0.044 0.503 2001 Planarity : 0.004 0.040 2300 Dihedral : 4.948 52.847 2100 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 0.57 % Allowed : 11.02 % Favored : 88.41 % 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: -0.56 (0.21), residues: 1631 helix: -0.05 (0.45), residues: 146 sheet: -0.06 (0.22), residues: 541 loop : -0.55 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 489 TYR 0.017 0.001 TYR B 178 PHE 0.010 0.001 PHE A 191 TRP 0.010 0.001 TRP A 58 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (13029) covalent geometry : angle 0.52312 / 0.26 (17705) SS BOND : bond 0.00192 / 0.12 ( 33) SS BOND : angle 0.54014 / 0.36 ( 66) hydrogen bonds : bond 0.02619 / 1.80 ( 425) hydrogen bonds : angle 5.63447 / 3.81 ( 1155) link_ALPHA1-3 : bond 0.01031 / 0.49 ( 1) link_ALPHA1-3 : angle 1.55785 / 0.51 ( 3) link_ALPHA1-4 : bond 0.00706 / 0.34 ( 3) link_ALPHA1-4 : angle 2.40090 / 1.14 ( 9) link_BETA1-4 : bond 0.00362 / 0.19 ( 5) link_BETA1-4 : angle 2.00288 / 1.06 ( 15) link_NAG-ASN : bond 0.00683 / 0.35 ( 7) link_NAG-ASN : angle 3.64227 / 2.64 ( 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 80 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.636 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: A 8 LEU cc_start: 0.8267 (mp) cc_final: 0.7851 (mt) REVERT: B 124 MET cc_start: 0.7614 (mmt) cc_final: 0.7174 (mmt) REVERT: B 568 MET cc_start: 0.5490 (tpp) cc_final: 0.4410 (tpp) REVERT: H 122 MET cc_start: 0.7586 (mtt) cc_final: 0.7282 (mtt) REVERT: L 107 ILE cc_start: 0.9195 (mp) cc_final: 0.8720 (tp) outliers start: 8 outliers final: 5 residues processed: 78 average time/residue: 1.1376 time to fit residues: 99.2199 Evaluate side-chains 76 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR 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 387 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 143 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.110105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.081886 restraints weight = 111295.781| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.69 r_work: 0.3604 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13078 Z= 0.177 Angle : 0.579 10.183 17819 Z= 0.283 Chirality : 0.044 0.500 2001 Planarity : 0.004 0.041 2300 Dihedral : 5.038 53.085 2100 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 0.86 % Allowed : 10.87 % Favored : 88.27 % 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: -0.11 (0.45), residues: 146 sheet: -0.16 (0.22), residues: 551 loop : -0.64 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 56 TYR 0.025 0.001 TYR B 178 PHE 0.014 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 0.00386 / 0.18 (13029) covalent geometry : angle 0.55787 / 0.28 (17705) SS BOND : bond 0.00266 / 0.15 ( 33) SS BOND : angle 0.69773 / 0.46 ( 66) hydrogen bonds : bond 0.02895 / 1.96 ( 425) hydrogen bonds : angle 5.72328 / 3.87 ( 1155) link_ALPHA1-3 : bond 0.00969 / 0.46 ( 1) link_ALPHA1-3 : angle 1.56266 / 0.49 ( 3) link_ALPHA1-4 : bond 0.00599 / 0.29 ( 3) link_ALPHA1-4 : angle 2.28852 / 1.14 ( 9) link_BETA1-4 : bond 0.00285 / 0.15 ( 5) link_BETA1-4 : angle 2.08794 / 1.10 ( 15) link_NAG-ASN : bond 0.00708 / 0.36 ( 7) link_NAG-ASN : angle 3.86347 / 2.72 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8797.42 seconds wall clock time: 149 minutes 55.53 seconds (8995.53 seconds total)