Starting phenix.real_space_refine on Tue May 20 08:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4k_41885/05_2025/8u4k_41885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4k_41885/05_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_41885/05_2025/8u4k_41885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4k_41885/05_2025/8u4k_41885.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4k_41885/05_2025/8u4k_41885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4k_41885/05_2025/8u4k_41885_trim.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.84, per 1000 atoms: 0.52 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: 5.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.93 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: 6.52 Time building geometry restraints manager: 6.58 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: 2.730 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: 0.350 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 42.020 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (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 TRP 0.119 0.011 TRP B 452 HIS 0.011 0.001 HIS B 174 PHE 0.056 0.004 PHE B 173 TYR 0.095 0.004 TYR A 268 ARG 0.007 0.001 ARG B 103 Details of bonding type rmsd link_NAG-ASN : bond 0.04743 ( 13) link_NAG-ASN : angle 7.30158 ( 39) 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_ALPHA1-3 : bond 0.01913 ( 2) link_ALPHA1-3 : angle 8.18910 ( 6) hydrogen bonds : bond 0.20554 ( 190) hydrogen bonds : angle 9.70280 ( 357) SS BOND : bond 0.08077 ( 51) SS BOND : angle 3.23628 ( 102) covalent geometry : bond 0.01274 (10202) covalent geometry : angle 1.63704 (13838) *********************** 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 : 1.454 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: 0.8921 (mt) cc_final: 0.8646 (tp) REVERT: A 250 MET cc_start: 0.8294 (mtm) cc_final: 0.8062 (mpp) REVERT: A 366 LEU cc_start: 0.8517 (tp) cc_final: 0.8287 (mp) REVERT: B 112 TYR cc_start: 0.9023 (m-80) cc_final: 0.8625 (m-80) 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: 0.6307 (mptt) REVERT: C 96 ASP cc_start: 0.8736 (t0) cc_final: 0.8428 (m-30) outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.6256 time to fit residues: 110.7916 Evaluate side-chains 75 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.058858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.044894 restraints weight = 164680.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.047215 restraints weight = 73296.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048834 restraints weight = 41997.193| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10288 Z= 0.163 Angle : 0.873 17.754 14045 Z= 0.410 Chirality : 0.050 0.308 1616 Planarity : 0.005 0.046 1775 Dihedral : 13.425 83.245 2037 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.09 % Allowed : 1.49 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.23), residues: 1212 helix: -2.23 (0.58), residues: 69 sheet: -1.29 (0.37), residues: 150 loop : -0.29 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.015 0.001 HIS B 470 PHE 0.009 0.001 PHE B 577 TYR 0.009 0.002 TYR A 429 ARG 0.007 0.001 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 13) link_NAG-ASN : angle 3.89341 ( 39) link_ALPHA1-6 : bond 0.00822 ( 2) link_ALPHA1-6 : angle 1.63243 ( 6) link_BETA1-4 : bond 0.01252 ( 18) link_BETA1-4 : angle 5.73391 ( 54) link_ALPHA1-3 : bond 0.01548 ( 2) link_ALPHA1-3 : angle 2.27421 ( 6) hydrogen bonds : bond 0.05802 ( 190) hydrogen bonds : angle 8.26648 ( 357) SS BOND : bond 0.00383 ( 51) SS BOND : angle 1.22551 ( 102) covalent geometry : bond 0.00353 (10202) covalent geometry : angle 0.76682 (13838) *********************** 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 : 1.580 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: A 99 LEU cc_start: 0.8880 (mt) cc_final: 0.8582 (tp) REVERT: A 366 LEU cc_start: 0.8398 (tp) cc_final: 0.8117 (mp) REVERT: B 112 TYR cc_start: 0.8800 (m-80) cc_final: 0.8458 (m-80) REVERT: C 79 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6950 (mptt) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.5229 time to fit residues: 71.2902 Evaluate side-chains 69 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 42 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN B 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.057536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.043601 restraints weight = 167991.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.045776 restraints weight = 76542.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.047334 restraints weight = 44613.859| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10288 Z= 0.166 Angle : 0.759 14.309 14045 Z= 0.362 Chirality : 0.049 0.299 1616 Planarity : 0.005 0.074 1775 Dihedral : 9.491 67.317 2037 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1212 helix: -2.60 (0.50), residues: 82 sheet: -1.26 (0.41), residues: 125 loop : -0.52 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 198 HIS 0.009 0.001 HIS B 470 PHE 0.010 0.001 PHE B 577 TYR 0.011 0.001 TYR B 303 ARG 0.004 0.001 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 13) link_NAG-ASN : angle 2.80253 ( 39) link_ALPHA1-6 : bond 0.00952 ( 2) link_ALPHA1-6 : angle 1.73839 ( 6) link_BETA1-4 : bond 0.01365 ( 18) link_BETA1-4 : angle 4.60662 ( 54) link_ALPHA1-3 : bond 0.01823 ( 2) link_ALPHA1-3 : angle 2.84066 ( 6) hydrogen bonds : bond 0.04986 ( 190) hydrogen bonds : angle 7.60345 ( 357) SS BOND : bond 0.00470 ( 51) SS BOND : angle 1.21820 ( 102) covalent geometry : bond 0.00351 (10202) covalent geometry : angle 0.68094 (13838) *********************** 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 89 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8931 (mt) cc_final: 0.8636 (tp) REVERT: A 366 LEU cc_start: 0.8460 (tp) cc_final: 0.8130 (mp) REVERT: B 112 TYR cc_start: 0.8907 (m-80) cc_final: 0.8656 (m-80) REVERT: B 326 ASP cc_start: 0.7957 (m-30) cc_final: 0.7244 (p0) outliers start: 2 outliers final: 2 residues processed: 89 average time/residue: 0.5157 time to fit residues: 63.2451 Evaluate side-chains 64 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 152 ASN B 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.057826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.043747 restraints weight = 166445.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.045908 restraints weight = 75823.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.047447 restraints weight = 44436.726| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10288 Z= 0.113 Angle : 0.674 13.640 14045 Z= 0.320 Chirality : 0.046 0.288 1616 Planarity : 0.004 0.049 1775 Dihedral : 7.697 56.388 2037 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1212 helix: -2.58 (0.50), residues: 82 sheet: -1.45 (0.39), residues: 137 loop : -0.49 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 474 HIS 0.006 0.001 HIS B 470 PHE 0.018 0.001 PHE B 173 TYR 0.008 0.001 TYR A 148 ARG 0.002 0.000 ARG C 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 13) link_NAG-ASN : angle 2.44001 ( 39) link_ALPHA1-6 : bond 0.00805 ( 2) link_ALPHA1-6 : angle 1.59558 ( 6) link_BETA1-4 : bond 0.01216 ( 18) link_BETA1-4 : angle 4.18733 ( 54) link_ALPHA1-3 : bond 0.01651 ( 2) link_ALPHA1-3 : angle 2.63115 ( 6) hydrogen bonds : bond 0.04172 ( 190) hydrogen bonds : angle 7.05625 ( 357) SS BOND : bond 0.00336 ( 51) SS BOND : angle 1.02541 ( 102) covalent geometry : bond 0.00243 (10202) covalent geometry : angle 0.60340 (13838) *********************** 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 78 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 1.448 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 60 MET cc_start: 0.8354 (mmp) cc_final: 0.8145 (mmp) REVERT: A 366 LEU cc_start: 0.8383 (tp) cc_final: 0.8070 (mp) REVERT: B 112 TYR cc_start: 0.8838 (m-80) cc_final: 0.8629 (m-80) REVERT: B 326 ASP cc_start: 0.8017 (m-30) cc_final: 0.7294 (p0) outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.5566 time to fit residues: 59.7644 Evaluate side-chains 64 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 471 ASN 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 = 0.056318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.042366 restraints weight = 172643.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.044373 restraints weight = 80111.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.045790 restraints weight = 47900.715| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10288 Z= 0.150 Angle : 0.667 12.322 14045 Z= 0.324 Chirality : 0.045 0.273 1616 Planarity : 0.004 0.059 1775 Dihedral : 6.653 41.677 2037 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.19 % Allowed : 1.12 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1212 helix: -2.45 (0.50), residues: 81 sheet: -1.44 (0.42), residues: 127 loop : -0.48 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 198 HIS 0.013 0.002 HIS B 237 PHE 0.021 0.001 PHE A 414 TYR 0.011 0.001 TYR B 303 ARG 0.003 0.001 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 13) link_NAG-ASN : angle 2.20390 ( 39) link_ALPHA1-6 : bond 0.00797 ( 2) link_ALPHA1-6 : angle 1.44067 ( 6) link_BETA1-4 : bond 0.01101 ( 18) link_BETA1-4 : angle 3.74912 ( 54) link_ALPHA1-3 : bond 0.01636 ( 2) link_ALPHA1-3 : angle 2.96623 ( 6) hydrogen bonds : bond 0.04141 ( 190) hydrogen bonds : angle 6.89764 ( 357) SS BOND : bond 0.00416 ( 51) SS BOND : angle 1.13197 ( 102) covalent geometry : bond 0.00317 (10202) covalent geometry : angle 0.60759 (13838) *********************** 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 74 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 1.533 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 81 ARG cc_start: 0.7214 (mtm110) cc_final: 0.6957 (mtt180) REVERT: A 366 LEU cc_start: 0.8511 (tp) cc_final: 0.8202 (mp) REVERT: B 326 ASP cc_start: 0.8065 (m-30) cc_final: 0.7339 (p0) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.5505 time to fit residues: 55.6843 Evaluate side-chains 56 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.057234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.043314 restraints weight = 170815.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.045415 restraints weight = 78164.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.046884 restraints weight = 45932.044| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4098 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= 0.097 Angle : 0.613 12.312 14045 Z= 0.295 Chirality : 0.045 0.259 1616 Planarity : 0.004 0.050 1775 Dihedral : 6.339 43.556 2037 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1212 helix: -2.17 (0.54), residues: 75 sheet: -1.35 (0.41), residues: 130 loop : -0.53 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS B 470 PHE 0.018 0.001 PHE A 447 TYR 0.015 0.001 TYR B 411 ARG 0.002 0.000 ARG B 203 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 13) link_NAG-ASN : angle 1.98917 ( 39) link_ALPHA1-6 : bond 0.00796 ( 2) link_ALPHA1-6 : angle 1.43916 ( 6) link_BETA1-4 : bond 0.01118 ( 18) link_BETA1-4 : angle 3.58077 ( 54) link_ALPHA1-3 : bond 0.01725 ( 2) link_ALPHA1-3 : angle 3.13279 ( 6) hydrogen bonds : bond 0.03613 ( 190) hydrogen bonds : angle 6.62576 ( 357) SS BOND : bond 0.00322 ( 51) SS BOND : angle 0.94815 ( 102) covalent geometry : bond 0.00207 (10202) covalent geometry : angle 0.55571 (13838) *********************** 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 73 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 1.406 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 81 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6949 (mtt180) REVERT: A 366 LEU cc_start: 0.8447 (tp) cc_final: 0.8142 (mp) REVERT: B 326 ASP cc_start: 0.8005 (m-30) cc_final: 0.7276 (p0) outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.5159 time to fit residues: 52.2478 Evaluate side-chains 61 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 152 ASN A 570 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.056098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.042279 restraints weight = 173871.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.044283 restraints weight = 79844.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.045603 restraints weight = 47298.417| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10288 Z= 0.146 Angle : 0.628 11.828 14045 Z= 0.305 Chirality : 0.044 0.246 1616 Planarity : 0.004 0.049 1775 Dihedral : 6.187 42.204 2037 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.23), residues: 1212 helix: -2.37 (0.51), residues: 81 sheet: -1.50 (0.42), residues: 127 loop : -0.56 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 198 HIS 0.004 0.001 HIS B 267 PHE 0.017 0.001 PHE B 425 TYR 0.011 0.001 TYR B 83 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 13) link_NAG-ASN : angle 2.12272 ( 39) link_ALPHA1-6 : bond 0.00778 ( 2) link_ALPHA1-6 : angle 1.38340 ( 6) link_BETA1-4 : bond 0.01085 ( 18) link_BETA1-4 : angle 3.47259 ( 54) link_ALPHA1-3 : bond 0.01564 ( 2) link_ALPHA1-3 : angle 3.18420 ( 6) hydrogen bonds : bond 0.03899 ( 190) hydrogen bonds : angle 6.63573 ( 357) SS BOND : bond 0.00469 ( 51) SS BOND : angle 1.00184 ( 102) covalent geometry : bond 0.00310 (10202) covalent geometry : angle 0.57275 (13838) *********************** 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 71 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 1.525 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8526 (tp) cc_final: 0.8214 (mp) REVERT: B 326 ASP cc_start: 0.8057 (m-30) cc_final: 0.7308 (p0) outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.5482 time to fit residues: 54.0319 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 : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 B 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.055860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.041961 restraints weight = 176636.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.043952 restraints weight = 81702.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.045318 restraints weight = 48556.165| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10288 Z= 0.142 Angle : 0.624 11.586 14045 Z= 0.306 Chirality : 0.044 0.233 1616 Planarity : 0.004 0.041 1775 Dihedral : 6.243 43.377 2037 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1212 helix: -2.30 (0.51), residues: 81 sheet: -1.61 (0.43), residues: 127 loop : -0.63 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 198 HIS 0.004 0.001 HIS B 267 PHE 0.012 0.001 PHE B 577 TYR 0.010 0.001 TYR B 303 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 13) link_NAG-ASN : angle 2.01918 ( 39) link_ALPHA1-6 : bond 0.00754 ( 2) link_ALPHA1-6 : angle 1.39553 ( 6) link_BETA1-4 : bond 0.01051 ( 18) link_BETA1-4 : angle 3.35809 ( 54) link_ALPHA1-3 : bond 0.01614 ( 2) link_ALPHA1-3 : angle 3.17463 ( 6) hydrogen bonds : bond 0.03800 ( 190) hydrogen bonds : angle 6.58110 ( 357) SS BOND : bond 0.00373 ( 51) SS BOND : angle 1.14363 ( 102) covalent geometry : bond 0.00302 (10202) covalent geometry : angle 0.57050 (13838) *********************** 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 71 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8546 (tp) cc_final: 0.8221 (mp) REVERT: B 326 ASP cc_start: 0.8094 (m-30) cc_final: 0.7318 (p0) outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 0.5329 time to fit residues: 52.3869 Evaluate side-chains 59 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 274 GLN ** 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 = 0.3704 r_free = 0.3704 target = 0.055138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.041188 restraints weight = 175943.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.043050 restraints weight = 84155.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.044355 restraints weight = 51185.195| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10288 Z= 0.153 Angle : 0.634 11.236 14045 Z= 0.311 Chirality : 0.044 0.222 1616 Planarity : 0.004 0.035 1775 Dihedral : 6.285 44.193 2037 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.19 % Allowed : 0.28 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.24), residues: 1212 helix: -2.33 (0.51), residues: 81 sheet: -1.71 (0.43), residues: 127 loop : -0.69 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 198 HIS 0.006 0.001 HIS B 249 PHE 0.015 0.001 PHE B 425 TYR 0.011 0.001 TYR A 96 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 13) link_NAG-ASN : angle 2.15282 ( 39) link_ALPHA1-6 : bond 0.00735 ( 2) link_ALPHA1-6 : angle 1.38428 ( 6) link_BETA1-4 : bond 0.01024 ( 18) link_BETA1-4 : angle 3.29207 ( 54) link_ALPHA1-3 : bond 0.01547 ( 2) link_ALPHA1-3 : angle 3.13651 ( 6) hydrogen bonds : bond 0.03944 ( 190) hydrogen bonds : angle 6.67454 ( 357) SS BOND : bond 0.00373 ( 51) SS BOND : angle 1.07202 ( 102) covalent geometry : bond 0.00329 (10202) covalent geometry : angle 0.58175 (13838) *********************** 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 66 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.7717 (t0) cc_final: 0.6629 (m-30) REVERT: A 60 MET cc_start: 0.8435 (mmm) cc_final: 0.8063 (mmp) REVERT: A 81 ARG cc_start: 0.7238 (mtm110) cc_final: 0.6988 (mtt180) REVERT: A 322 MET cc_start: 0.6953 (pmm) cc_final: 0.6713 (pmm) REVERT: A 366 LEU cc_start: 0.8653 (tp) cc_final: 0.8314 (mp) REVERT: B 326 ASP cc_start: 0.8042 (m-30) cc_final: 0.7246 (p0) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.5959 time to fit residues: 55.0791 Evaluate side-chains 56 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.056101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.042237 restraints weight = 175449.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.044237 restraints weight = 81052.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.045619 restraints weight = 48224.664| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4904 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= 0.095 Angle : 0.593 11.012 14045 Z= 0.287 Chirality : 0.044 0.216 1616 Planarity : 0.004 0.037 1775 Dihedral : 6.006 42.979 2037 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.19 % Allowed : 0.00 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1212 helix: -2.11 (0.55), residues: 81 sheet: -1.61 (0.43), residues: 120 loop : -0.63 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 198 HIS 0.003 0.001 HIS B 469 PHE 0.019 0.001 PHE B 400 TYR 0.009 0.001 TYR A 148 ARG 0.003 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 13) link_NAG-ASN : angle 1.83659 ( 39) link_ALPHA1-6 : bond 0.00707 ( 2) link_ALPHA1-6 : angle 1.39746 ( 6) link_BETA1-4 : bond 0.01044 ( 18) link_BETA1-4 : angle 3.16531 ( 54) link_ALPHA1-3 : bond 0.01516 ( 2) link_ALPHA1-3 : angle 3.09477 ( 6) hydrogen bonds : bond 0.03333 ( 190) hydrogen bonds : angle 6.37628 ( 357) SS BOND : bond 0.00260 ( 51) SS BOND : angle 0.88195 ( 102) covalent geometry : bond 0.00208 (10202) covalent geometry : angle 0.54554 (13838) ********************** 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 66 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.540 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 60 MET cc_start: 0.8423 (mmm) cc_final: 0.8029 (mmp) REVERT: A 366 LEU cc_start: 0.8525 (tp) cc_final: 0.8196 (mp) REVERT: B 326 ASP cc_start: 0.8070 (m-30) cc_final: 0.7262 (p0) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.5588 time to fit residues: 50.4307 Evaluate side-chains 56 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 58 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.055828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.042047 restraints weight = 174005.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.044021 restraints weight = 79833.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.045372 restraints weight = 47376.795| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10288 Z= 0.109 Angle : 0.582 10.692 14045 Z= 0.283 Chirality : 0.043 0.213 1616 Planarity : 0.004 0.039 1775 Dihedral : 5.870 42.567 2037 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1212 helix: -2.08 (0.55), residues: 81 sheet: -1.63 (0.46), residues: 110 loop : -0.62 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 PHE 0.010 0.001 PHE B 376 TYR 0.009 0.001 TYR A 148 ARG 0.002 0.000 ARG B 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 13) link_NAG-ASN : angle 1.94029 ( 39) link_ALPHA1-6 : bond 0.00691 ( 2) link_ALPHA1-6 : angle 1.38644 ( 6) link_BETA1-4 : bond 0.01023 ( 18) link_BETA1-4 : angle 3.13278 ( 54) link_ALPHA1-3 : bond 0.01470 ( 2) link_ALPHA1-3 : angle 2.98227 ( 6) hydrogen bonds : bond 0.03421 ( 190) hydrogen bonds : angle 6.38363 ( 357) SS BOND : bond 0.00286 ( 51) SS BOND : angle 0.87104 ( 102) covalent geometry : bond 0.00235 (10202) covalent geometry : angle 0.53395 (13838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5632.79 seconds wall clock time: 98 minutes 2.88 seconds (5882.88 seconds total)