Starting phenix.real_space_refine on Sun Aug 24 12:08:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4k_41885/08_2025/8u4k_41885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4k_41885/08_2025/8u4k_41885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4k_41885/08_2025/8u4k_41885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4k_41885/08_2025/8u4k_41885.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4k_41885/08_2025/8u4k_41885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4k_41885/08_2025/8u4k_41885_trim.cif" } resolution = 4.27 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= -0.000 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 116 5.16 5 C 6182 2.51 5 N 1713 2.21 5 O 1978 1.98 5 H 9074 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19063 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 9060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 9060 Classifications: {'peptide': 598} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 570} Chain breaks: 3 Chain: "B" Number of atoms: 8787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 8787 Classifications: {'peptide': 582} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 543} Chain breaks: 2 Chain: "C" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 762 Classifications: {'peptide': 48} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, '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: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, '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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.19 Number of scatterers: 19063 At special positions: 0 Unit cell: (83.5, 132.765, 140.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 1978 8.00 N 1713 7.00 C 6182 6.00 H 9074 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.09 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.06 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.07 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=2.02 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.00 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.01 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.04 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.01 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.02 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.08 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.05 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.01 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.00 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=1.75 Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.02 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.17 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.02 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.22 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.05 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.02 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.15 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.00 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.01 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.01 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.01 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=1.72 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.19 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.13 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.16 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.01 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.02 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.01 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.02 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 82 " distance=2.16 Simple disulfide: pdb=" SG CYS C 77 " - pdb=" SG CYS C 93 " distance=2.01 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 104 " distance=2.01 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 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA G 3 " - " MAN G 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 701 " - " ASN A 410 " " NAG A 702 " - " ASN A 495 " " NAG B 701 " - " ASN B 68 " " NAG D 1 " - " ASN A 138 " " NAG E 1 " - " ASN A 358 " " NAG F 1 " - " ASN A 473 " " NAG G 1 " - " ASN A 576 " " NAG H 1 " - " ASN A 548 " " NAG I 1 " - " ASN A 253 " " NAG J 1 " - " ASN B 187 " " NAG K 1 " - " ASN B 259 " " NAG L 1 " - " ASN B 530 " " NAG M 1 " - " ASN B 571 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 543.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 29 sheets defined 16.0% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.315A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.061A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 removed outlier: 4.085A pdb=" N CYS A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.918A pdb=" N MET A 343 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.109A pdb=" N ILE A 357 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.289A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 removed outlier: 4.531A pdb=" N HIS A 470 " --> pdb=" O CYS A 467 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 472 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.911A pdb=" N CYS A 520 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 removed outlier: 3.924A pdb=" N CYS A 633 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.240A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.813A pdb=" N ILE B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 removed outlier: 4.234A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 365 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 481 through 486 removed outlier: 3.665A pdb=" N LEU B 485 " --> pdb=" O PRO B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 506 through 508 No H-bonds generated for 'chain 'B' and resid 506 through 508' Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'C' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.932A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 7.216A pdb=" N SER A 38 " --> pdb=" O CYS C 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 4.791A pdb=" N TYR A 115 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A 148 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 117 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASP A 150 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ILE A 119 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 177 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 238 removed outlier: 7.601A pdb=" N GLY A 237 " --> pdb=" O CYS A 246 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N CYS A 246 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 269 removed outlier: 3.556A pdb=" N GLN A 274 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 283 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 317 Processing sheet with id=AB1, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.242A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 423 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 366 through 368 removed outlier: 7.770A pdb=" N TYR A 459 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 435 " --> pdb=" O TYR A 459 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR A 461 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A 437 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 488 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 528 Processing sheet with id=AB4, first strand: chain 'A' and resid 545 through 547 Processing sheet with id=AB5, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.506A pdb=" N ASN A 588 " --> pdb=" O ASP A 585 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 606 through 608 Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 27 removed outlier: 7.012A pdb=" N CYS B 26 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63 removed outlier: 7.672A pdb=" N LEU B 154 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 115 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLN B 156 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 117 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 244 removed outlier: 7.563A pdb=" N GLY B 243 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N CYS B 252 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 263 through 265 removed outlier: 7.013A pdb=" N ASN B 259 " --> pdb=" O CYS B 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 275 removed outlier: 3.656A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 306 removed outlier: 3.573A pdb=" N SER B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC5, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AC6, first strand: chain 'B' and resid 374 through 376 removed outlier: 4.533A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 534 through 536 Processing sheet with id=AC8, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AC9, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AD1, first strand: chain 'B' and resid 615 through 617 Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 100 190 hydrogen bonds defined for protein. 357 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: 3.31 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9073 1.13 - 1.30: 1721 1.30 - 1.48: 3966 1.48 - 1.65: 4387 1.65 - 1.82: 129 Bond restraints: 19276 Sorted by residual: bond pdb=" NE2 GLN B 239 " pdb="HE21 GLN B 239 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASP A 335 " pdb=" H ASP A 335 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD1 TYR B 163 " pdb=" HD1 TYR B 163 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 PHE A 120 " pdb=" HE1 PHE A 120 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ASP B 592 " pdb=" H ASP B 592 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 19271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 31640 3.41 - 6.83: 2688 6.83 - 10.24: 211 10.24 - 13.66: 1 13.66 - 17.07: 1 Bond angle restraints: 34541 Sorted by residual: angle pdb=" N PHE B 577 " pdb=" CA PHE B 577 " pdb=" C PHE B 577 " ideal model delta sigma weight residual 108.20 125.27 -17.07 1.71e+00 3.42e-01 9.97e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 110.62 117.04 -6.42 1.02e+00 9.61e-01 3.97e+01 angle pdb=" C GLU B 265 " pdb=" N LEU B 266 " pdb=" CA LEU B 266 " ideal model delta sigma weight residual 120.28 128.40 -8.12 1.34e+00 5.57e-01 3.67e+01 angle pdb=" C ASP A 150 " pdb=" CA ASP A 150 " pdb=" CB ASP A 150 " ideal model delta sigma weight residual 116.54 109.64 6.90 1.15e+00 7.56e-01 3.60e+01 angle pdb=" C ARG A 525 " pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " ideal model delta sigma weight residual 117.23 109.18 8.05 1.36e+00 5.41e-01 3.50e+01 ... (remaining 34536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.40: 9030 21.40 - 42.80: 428 42.80 - 64.19: 230 64.19 - 85.59: 69 85.59 - 106.99: 34 Dihedral angle restraints: 9791 sinusoidal: 5671 harmonic: 4120 Sorted by residual: dihedral pdb=" CB CYS B 315 " pdb=" SG CYS B 315 " pdb=" SG CYS B 331 " pdb=" CB CYS B 331 " ideal model delta sinusoidal sigma weight residual -86.00 -174.11 88.11 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS A 217 " pdb=" SG CYS A 217 " pdb=" SG CYS A 229 " pdb=" CB CYS A 229 " ideal model delta sinusoidal sigma weight residual 93.00 176.27 -83.27 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS A 293 " pdb=" SG CYS A 293 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual -86.00 -159.09 73.09 1 1.00e+01 1.00e-02 6.81e+01 ... (remaining 9788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1326 0.107 - 0.214: 254 0.214 - 0.322: 19 0.322 - 0.429: 14 0.429 - 0.536: 3 Chirality restraints: 1616 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.97 0.43 2.00e-02 2.50e+03 4.64e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-02 2.50e+03 4.57e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.22e+02 ... (remaining 1613 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG D 1 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.111 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.311 2.00e-02 2.50e+03 2.69e-01 9.06e+02 pdb=" C7 NAG G 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.026 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.294 2.00e-02 2.50e+03 2.48e-01 7.66e+02 pdb=" C7 NAG D 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.186 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.422 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.025 2.00e-02 2.50e+03 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1557 2.19 - 2.79: 33757 2.79 - 3.39: 50708 3.39 - 4.00: 67985 4.00 - 4.60: 98080 Nonbonded interactions: 252087 Sorted by model distance: nonbonded pdb=" HG1 THR A 471 " pdb=" O CYS A 512 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU B 321 " pdb=" HZ1 LYS B 369 " model vdw 1.585 2.450 nonbonded pdb="HE21 GLN A 216 " pdb=" O CYS B 235 " model vdw 1.592 2.450 nonbonded pdb=" HH TYR A 123 " pdb=" OE1 GLN A 151 " model vdw 1.616 2.450 nonbonded pdb=" OE2 GLU B 405 " pdb=" HE ARG B 432 " model vdw 1.625 2.450 ... (remaining 252082 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 'D' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.014 0.316 10288 Z= 0.850 Angle : 1.775 22.222 14045 Z= 1.116 Chirality : 0.088 0.536 1616 Planarity : 0.016 0.300 1775 Dihedral : 16.015 106.989 4294 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.19 % Allowed : 1.21 % Favored : 98.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1212 helix: -3.10 (0.49), residues: 69 sheet: -1.23 (0.47), residues: 99 loop : -0.13 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 103 TYR 0.095 0.004 TYR A 268 PHE 0.056 0.004 PHE B 173 TRP 0.119 0.011 TRP B 452 HIS 0.011 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.01274 (10202) covalent geometry : angle 1.63704 (13838) SS BOND : bond 0.08077 ( 51) SS BOND : angle 3.23628 ( 102) hydrogen bonds : bond 0.20554 ( 190) hydrogen bonds : angle 9.70280 ( 357) link_ALPHA1-3 : bond 0.01913 ( 2) link_ALPHA1-3 : angle 8.18910 ( 6) link_ALPHA1-6 : bond 0.01924 ( 2) link_ALPHA1-6 : angle 2.97100 ( 6) link_BETA1-4 : bond 0.02832 ( 18) link_BETA1-4 : angle 8.11345 ( 54) link_NAG-ASN : bond 0.04743 ( 13) link_NAG-ASN : angle 7.30158 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.554 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 99 LEU cc_start: 0.8921 (mt) cc_final: 0.8646 (tp) REVERT: A 218 ASP cc_start: 0.8298 (m-30) cc_final: 0.8043 (m-30) REVERT: A 250 MET cc_start: 0.8294 (mtm) cc_final: 0.8063 (mpp) REVERT: A 366 LEU cc_start: 0.8517 (tp) cc_final: 0.8287 (mp) REVERT: B 326 ASP cc_start: 0.8010 (m-30) cc_final: 0.7213 (p0) REVERT: C 79 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6306 (mptt) REVERT: C 96 ASP cc_start: 0.8736 (t0) cc_final: 0.8427 (m-30) outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.3104 time to fit residues: 54.1671 Evaluate side-chains 74 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN B 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.058960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.044964 restraints weight = 164613.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.047284 restraints weight = 73230.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.048904 restraints weight = 42022.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.050013 restraints weight = 28418.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.050712 restraints weight = 21339.884| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10288 Z= 0.167 Angle : 0.872 17.117 14045 Z= 0.406 Chirality : 0.050 0.307 1616 Planarity : 0.005 0.046 1775 Dihedral : 13.066 82.255 2037 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 1.40 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.23), residues: 1212 helix: -2.25 (0.58), residues: 69 sheet: -1.18 (0.37), residues: 140 loop : -0.33 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.012 0.002 TYR B 112 PHE 0.009 0.001 PHE B 258 TRP 0.015 0.001 TRP A 171 HIS 0.015 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00367 (10202) covalent geometry : angle 0.76995 (13838) SS BOND : bond 0.00372 ( 51) SS BOND : angle 1.15833 ( 102) hydrogen bonds : bond 0.05464 ( 190) hydrogen bonds : angle 8.17802 ( 357) link_ALPHA1-3 : bond 0.01534 ( 2) link_ALPHA1-3 : angle 2.09080 ( 6) link_ALPHA1-6 : bond 0.00738 ( 2) link_ALPHA1-6 : angle 1.62695 ( 6) link_BETA1-4 : bond 0.01200 ( 18) link_BETA1-4 : angle 5.64096 ( 54) link_NAG-ASN : bond 0.00700 ( 13) link_NAG-ASN : angle 3.81501 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.500 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 99 LEU cc_start: 0.8860 (mt) cc_final: 0.8568 (tp) REVERT: A 366 LEU cc_start: 0.8358 (tp) cc_final: 0.8088 (mp) REVERT: B 112 TYR cc_start: 0.8872 (m-80) cc_final: 0.8595 (m-80) REVERT: C 79 LYS cc_start: 0.7259 (mmtt) cc_final: 0.6934 (mptt) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2295 time to fit residues: 31.3726 Evaluate side-chains 70 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.058177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.044080 restraints weight = 168256.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.046319 restraints weight = 76184.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.047897 restraints weight = 44333.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.048983 restraints weight = 30356.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.049661 restraints weight = 23031.962| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10288 Z= 0.141 Angle : 0.738 14.488 14045 Z= 0.349 Chirality : 0.049 0.298 1616 Planarity : 0.004 0.056 1775 Dihedral : 9.521 68.217 2037 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.23), residues: 1212 helix: -2.38 (0.53), residues: 76 sheet: -1.30 (0.38), residues: 140 loop : -0.46 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 330 TYR 0.009 0.001 TYR B 112 PHE 0.010 0.001 PHE B 577 TRP 0.012 0.001 TRP A 198 HIS 0.010 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00301 (10202) covalent geometry : angle 0.65839 (13838) SS BOND : bond 0.00418 ( 51) SS BOND : angle 1.00960 ( 102) hydrogen bonds : bond 0.04806 ( 190) hydrogen bonds : angle 7.58957 ( 357) link_ALPHA1-3 : bond 0.01658 ( 2) link_ALPHA1-3 : angle 2.89960 ( 6) link_ALPHA1-6 : bond 0.00772 ( 2) link_ALPHA1-6 : angle 1.69404 ( 6) link_BETA1-4 : bond 0.01343 ( 18) link_BETA1-4 : angle 4.66716 ( 54) link_NAG-ASN : bond 0.00480 ( 13) link_NAG-ASN : angle 2.78381 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.549 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: A 99 LEU cc_start: 0.8903 (mt) cc_final: 0.8628 (tp) REVERT: A 366 LEU cc_start: 0.8384 (tp) cc_final: 0.8089 (mp) REVERT: B 112 TYR cc_start: 0.8908 (m-80) cc_final: 0.8692 (m-80) REVERT: B 326 ASP cc_start: 0.7772 (m-30) cc_final: 0.7091 (p0) outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.2418 time to fit residues: 29.9858 Evaluate side-chains 68 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 122 ASN A 152 ASN B 320 GLN B 471 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.056984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.042942 restraints weight = 172171.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.045014 restraints weight = 79545.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.046478 restraints weight = 47259.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.047532 restraints weight = 32768.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.048123 restraints weight = 25178.150| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10288 Z= 0.165 Angle : 0.702 13.441 14045 Z= 0.337 Chirality : 0.046 0.283 1616 Planarity : 0.004 0.049 1775 Dihedral : 7.442 51.313 2037 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.19 % Allowed : 0.84 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.23), residues: 1212 helix: -2.24 (0.53), residues: 75 sheet: -1.38 (0.42), residues: 127 loop : -0.52 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.010 0.001 TYR B 303 PHE 0.027 0.002 PHE B 173 TRP 0.025 0.002 TRP A 474 HIS 0.006 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00348 (10202) covalent geometry : angle 0.63417 (13838) SS BOND : bond 0.00454 ( 51) SS BOND : angle 1.19816 ( 102) hydrogen bonds : bond 0.04396 ( 190) hydrogen bonds : angle 7.07327 ( 357) link_ALPHA1-3 : bond 0.01734 ( 2) link_ALPHA1-3 : angle 2.54233 ( 6) link_ALPHA1-6 : bond 0.00795 ( 2) link_ALPHA1-6 : angle 1.51161 ( 6) link_BETA1-4 : bond 0.01221 ( 18) link_BETA1-4 : angle 4.10466 ( 54) link_NAG-ASN : bond 0.00406 ( 13) link_NAG-ASN : angle 2.47855 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.524 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 366 LEU cc_start: 0.8434 (tp) cc_final: 0.8125 (mp) REVERT: B 326 ASP cc_start: 0.7916 (m-30) cc_final: 0.7216 (p0) outliers start: 2 outliers final: 2 residues processed: 80 average time/residue: 0.2535 time to fit residues: 27.5062 Evaluate side-chains 60 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A 570 HIS B 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.056264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.042229 restraints weight = 171002.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.044205 restraints weight = 79629.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.045605 restraints weight = 47723.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.046580 restraints weight = 33351.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.047141 restraints weight = 26064.991| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10288 Z= 0.159 Angle : 0.673 12.808 14045 Z= 0.325 Chirality : 0.045 0.270 1616 Planarity : 0.004 0.044 1775 Dihedral : 7.019 58.468 2037 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.19 % Allowed : 0.93 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.23), residues: 1212 helix: -2.46 (0.50), residues: 81 sheet: -1.53 (0.42), residues: 127 loop : -0.53 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 114 TYR 0.010 0.001 TYR B 303 PHE 0.010 0.001 PHE B 577 TRP 0.011 0.001 TRP A 198 HIS 0.004 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00335 (10202) covalent geometry : angle 0.60944 (13838) SS BOND : bond 0.00428 ( 51) SS BOND : angle 1.17186 ( 102) hydrogen bonds : bond 0.04296 ( 190) hydrogen bonds : angle 6.98842 ( 357) link_ALPHA1-3 : bond 0.01783 ( 2) link_ALPHA1-3 : angle 2.95500 ( 6) link_ALPHA1-6 : bond 0.00788 ( 2) link_ALPHA1-6 : angle 1.49166 ( 6) link_BETA1-4 : bond 0.01127 ( 18) link_BETA1-4 : angle 3.82949 ( 54) link_NAG-ASN : bond 0.00310 ( 13) link_NAG-ASN : angle 2.38718 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.477 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 218 ASP cc_start: 0.8595 (m-30) cc_final: 0.8282 (m-30) REVERT: A 366 LEU cc_start: 0.8461 (tp) cc_final: 0.8140 (mp) REVERT: B 326 ASP cc_start: 0.7924 (m-30) cc_final: 0.7207 (p0) outliers start: 2 outliers final: 2 residues processed: 72 average time/residue: 0.2224 time to fit residues: 22.6368 Evaluate side-chains 58 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.055776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.041910 restraints weight = 173659.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.043843 restraints weight = 80466.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.045228 restraints weight = 48053.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.046171 restraints weight = 33405.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.046704 restraints weight = 26003.336| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10288 Z= 0.163 Angle : 0.662 12.484 14045 Z= 0.323 Chirality : 0.045 0.256 1616 Planarity : 0.004 0.042 1775 Dihedral : 6.746 44.501 2037 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.23), residues: 1212 helix: -2.45 (0.50), residues: 81 sheet: -1.64 (0.42), residues: 127 loop : -0.65 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 558 TYR 0.017 0.001 TYR B 411 PHE 0.016 0.001 PHE A 447 TRP 0.011 0.001 TRP A 198 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00346 (10202) covalent geometry : angle 0.60417 (13838) SS BOND : bond 0.00440 ( 51) SS BOND : angle 1.10612 ( 102) hydrogen bonds : bond 0.04216 ( 190) hydrogen bonds : angle 6.85531 ( 357) link_ALPHA1-3 : bond 0.01684 ( 2) link_ALPHA1-3 : angle 3.07072 ( 6) link_ALPHA1-6 : bond 0.00787 ( 2) link_ALPHA1-6 : angle 1.42371 ( 6) link_BETA1-4 : bond 0.01094 ( 18) link_BETA1-4 : angle 3.66584 ( 54) link_NAG-ASN : bond 0.00234 ( 13) link_NAG-ASN : angle 2.22003 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.512 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 366 LEU cc_start: 0.8532 (tp) cc_final: 0.8214 (mp) REVERT: B 326 ASP cc_start: 0.7938 (m-30) cc_final: 0.7212 (p0) outliers start: 2 outliers final: 2 residues processed: 76 average time/residue: 0.2090 time to fit residues: 22.2106 Evaluate side-chains 54 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 100 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 HIS B 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.056345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.042427 restraints weight = 172870.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.044418 restraints weight = 79904.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.045819 restraints weight = 47426.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.046792 restraints weight = 33003.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.047379 restraints weight = 25542.687| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10288 Z= 0.108 Angle : 0.617 12.092 14045 Z= 0.299 Chirality : 0.044 0.247 1616 Planarity : 0.004 0.044 1775 Dihedral : 6.441 43.237 2037 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.19 % Allowed : 0.09 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.23), residues: 1212 helix: -2.34 (0.51), residues: 81 sheet: -1.57 (0.42), residues: 127 loop : -0.57 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 558 TYR 0.009 0.001 TYR B 83 PHE 0.018 0.001 PHE B 425 TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00231 (10202) covalent geometry : angle 0.56043 (13838) SS BOND : bond 0.00327 ( 51) SS BOND : angle 1.01105 ( 102) hydrogen bonds : bond 0.03679 ( 190) hydrogen bonds : angle 6.66260 ( 357) link_ALPHA1-3 : bond 0.01706 ( 2) link_ALPHA1-3 : angle 3.18990 ( 6) link_ALPHA1-6 : bond 0.00784 ( 2) link_ALPHA1-6 : angle 1.40721 ( 6) link_BETA1-4 : bond 0.01088 ( 18) link_BETA1-4 : angle 3.49476 ( 54) link_NAG-ASN : bond 0.00254 ( 13) link_NAG-ASN : angle 2.06652 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.573 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 366 LEU cc_start: 0.8491 (tp) cc_final: 0.8168 (mp) REVERT: B 326 ASP cc_start: 0.7932 (m-30) cc_final: 0.7180 (p0) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.2288 time to fit residues: 21.8246 Evaluate side-chains 57 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 16 optimal weight: 0.0670 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN C 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.055390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.041347 restraints weight = 174652.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.043242 restraints weight = 83710.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.044527 restraints weight = 50647.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.045452 restraints weight = 35915.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.045924 restraints weight = 28096.333| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10288 Z= 0.146 Angle : 0.625 11.519 14045 Z= 0.305 Chirality : 0.044 0.232 1616 Planarity : 0.004 0.051 1775 Dihedral : 6.307 41.809 2037 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.19 % Allowed : 0.65 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.24), residues: 1212 helix: -2.23 (0.52), residues: 81 sheet: -1.67 (0.43), residues: 127 loop : -0.65 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 106 TYR 0.011 0.001 TYR B 303 PHE 0.023 0.001 PHE A 414 TRP 0.013 0.001 TRP A 198 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00310 (10202) covalent geometry : angle 0.57070 (13838) SS BOND : bond 0.00398 ( 51) SS BOND : angle 1.08525 ( 102) hydrogen bonds : bond 0.03850 ( 190) hydrogen bonds : angle 6.62690 ( 357) link_ALPHA1-3 : bond 0.01654 ( 2) link_ALPHA1-3 : angle 3.21150 ( 6) link_ALPHA1-6 : bond 0.00797 ( 2) link_ALPHA1-6 : angle 1.38281 ( 6) link_BETA1-4 : bond 0.01065 ( 18) link_BETA1-4 : angle 3.36476 ( 54) link_NAG-ASN : bond 0.00256 ( 13) link_NAG-ASN : angle 2.10128 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.525 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: A 366 LEU cc_start: 0.8601 (tp) cc_final: 0.8291 (mp) REVERT: B 326 ASP cc_start: 0.7903 (m-30) cc_final: 0.7121 (p0) outliers start: 2 outliers final: 2 residues processed: 67 average time/residue: 0.2426 time to fit residues: 22.4335 Evaluate side-chains 54 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 101 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.055247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.041227 restraints weight = 173264.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.043081 restraints weight = 83515.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.044387 restraints weight = 50772.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.045290 restraints weight = 35834.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.045934 restraints weight = 28199.053| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10288 Z= 0.134 Angle : 0.618 11.306 14045 Z= 0.302 Chirality : 0.044 0.223 1616 Planarity : 0.004 0.050 1775 Dihedral : 6.314 42.736 2037 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.19 % Allowed : 0.09 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.24), residues: 1212 helix: -2.21 (0.53), residues: 81 sheet: -1.77 (0.45), residues: 117 loop : -0.67 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.009 0.001 TYR B 303 PHE 0.011 0.001 PHE B 577 TRP 0.042 0.002 TRP A 198 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00287 (10202) covalent geometry : angle 0.56559 (13838) SS BOND : bond 0.00353 ( 51) SS BOND : angle 1.02979 ( 102) hydrogen bonds : bond 0.03707 ( 190) hydrogen bonds : angle 6.56262 ( 357) link_ALPHA1-3 : bond 0.01492 ( 2) link_ALPHA1-3 : angle 3.14240 ( 6) link_ALPHA1-6 : bond 0.00785 ( 2) link_ALPHA1-6 : angle 1.42836 ( 6) link_BETA1-4 : bond 0.01095 ( 18) link_BETA1-4 : angle 3.29764 ( 54) link_NAG-ASN : bond 0.00213 ( 13) link_NAG-ASN : angle 2.07100 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.541 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: A 366 LEU cc_start: 0.8624 (tp) cc_final: 0.8309 (mp) REVERT: B 326 ASP cc_start: 0.7841 (m-30) cc_final: 0.7031 (p0) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.2285 time to fit residues: 20.7686 Evaluate side-chains 55 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 65 optimal weight: 0.0980 chunk 71 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.055776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.041942 restraints weight = 175534.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.043917 restraints weight = 80877.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.045261 restraints weight = 48124.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.046204 restraints weight = 33556.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.046856 restraints weight = 26065.784| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10288 Z= 0.102 Angle : 0.590 10.970 14045 Z= 0.286 Chirality : 0.044 0.215 1616 Planarity : 0.004 0.047 1775 Dihedral : 6.044 42.753 2037 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.19 % Allowed : 0.09 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.24), residues: 1212 helix: -2.02 (0.56), residues: 81 sheet: -1.65 (0.43), residues: 127 loop : -0.59 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 558 TYR 0.010 0.001 TYR A 148 PHE 0.016 0.001 PHE B 425 TRP 0.027 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00221 (10202) covalent geometry : angle 0.54038 (13838) SS BOND : bond 0.00283 ( 51) SS BOND : angle 0.89195 ( 102) hydrogen bonds : bond 0.03426 ( 190) hydrogen bonds : angle 6.40567 ( 357) link_ALPHA1-3 : bond 0.01473 ( 2) link_ALPHA1-3 : angle 3.08393 ( 6) link_ALPHA1-6 : bond 0.00710 ( 2) link_ALPHA1-6 : angle 1.38683 ( 6) link_BETA1-4 : bond 0.01031 ( 18) link_BETA1-4 : angle 3.17853 ( 54) link_NAG-ASN : bond 0.00217 ( 13) link_NAG-ASN : angle 1.93815 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.497 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: A 60 MET cc_start: 0.8317 (mmm) cc_final: 0.7986 (mmp) REVERT: A 366 LEU cc_start: 0.8503 (tp) cc_final: 0.8197 (mp) REVERT: B 326 ASP cc_start: 0.7899 (m-30) cc_final: 0.7078 (p0) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.2494 time to fit residues: 21.5592 Evaluate side-chains 51 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.056173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.042309 restraints weight = 173553.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.044294 restraints weight = 79450.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.045679 restraints weight = 47041.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.046638 restraints weight = 32729.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.047262 restraints weight = 25256.402| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10288 Z= 0.093 Angle : 0.575 10.660 14045 Z= 0.277 Chirality : 0.043 0.212 1616 Planarity : 0.004 0.046 1775 Dihedral : 5.786 42.282 2037 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.19 % Allowed : 0.09 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.24), residues: 1212 helix: -1.97 (0.56), residues: 81 sheet: -1.59 (0.44), residues: 127 loop : -0.54 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 34 TYR 0.009 0.001 TYR A 148 PHE 0.011 0.001 PHE B 376 TRP 0.028 0.001 TRP A 198 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00203 (10202) covalent geometry : angle 0.52697 (13838) SS BOND : bond 0.00254 ( 51) SS BOND : angle 0.86401 ( 102) hydrogen bonds : bond 0.03193 ( 190) hydrogen bonds : angle 6.29427 ( 357) link_ALPHA1-3 : bond 0.01491 ( 2) link_ALPHA1-3 : angle 2.98669 ( 6) link_ALPHA1-6 : bond 0.00686 ( 2) link_ALPHA1-6 : angle 1.39471 ( 6) link_BETA1-4 : bond 0.01031 ( 18) link_BETA1-4 : angle 3.10468 ( 54) link_NAG-ASN : bond 0.00218 ( 13) link_NAG-ASN : angle 1.89170 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.91 seconds wall clock time: 54 minutes 3.69 seconds (3243.69 seconds total)