Starting phenix.real_space_refine on Tue Jun 17 08:59:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4k_41885/06_2025/8u4k_41885_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4k_41885/06_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_41885/06_2025/8u4k_41885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4k_41885/06_2025/8u4k_41885.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4k_41885/06_2025/8u4k_41885_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4k_41885/06_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-5710/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: 11.08, per 1000 atoms: 0.58 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: 5.76 Conformation dependent library (CDL) restraints added in 1.4 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: 1.83 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: 7.57 Time building geometry restraints manager: 6.52 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: 3.230 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: 0.380 Extract box with map and model: 0.930 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 46.110 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- 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 : 1.637 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: 0.6450 time to fit residues: 114.4739 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 : 1.530 ------------------------------------------------------------------------------- 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 = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.044897 restraints weight = 164680.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.047215 restraints weight = 73221.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.048846 restraints weight = 42021.200| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 1.775 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: 0.8878 (mt) cc_final: 0.8582 (tp) REVERT: A 366 LEU cc_start: 0.8398 (tp) cc_final: 0.8118 (mp) REVERT: B 112 TYR cc_start: 0.8804 (m-80) cc_final: 0.8460 (m-80) REVERT: C 79 LYS cc_start: 0.7279 (mmtt) cc_final: 0.6948 (mptt) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.5100 time to fit residues: 69.4956 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 : 1.493 ------------------------------------------------------------------------------- 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: 10.0000 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.057742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.043642 restraints weight = 168059.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.045823 restraints weight = 76631.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.047366 restraints weight = 44913.844| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10288 Z= 0.164 Angle : 0.762 14.269 14045 Z= 0.364 Chirality : 0.049 0.308 1616 Planarity : 0.005 0.068 1775 Dihedral : 9.725 68.625 2037 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: -1.06 (0.23), residues: 1212 helix: -2.38 (0.53), residues: 76 sheet: -1.25 (0.41), residues: 125 loop : -0.51 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 198 HIS 0.009 0.001 HIS B 470 PHE 0.010 0.001 PHE B 577 TYR 0.010 0.001 TYR B 303 ARG 0.005 0.001 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 13) link_NAG-ASN : angle 2.86834 ( 39) link_ALPHA1-6 : bond 0.00769 ( 2) link_ALPHA1-6 : angle 1.69730 ( 6) link_BETA1-4 : bond 0.01368 ( 18) link_BETA1-4 : angle 4.68135 ( 54) link_ALPHA1-3 : bond 0.01660 ( 2) link_ALPHA1-3 : angle 2.79135 ( 6) hydrogen bonds : bond 0.05007 ( 190) hydrogen bonds : angle 7.64649 ( 357) SS BOND : bond 0.00473 ( 51) SS BOND : angle 1.18817 ( 102) covalent geometry : bond 0.00349 (10202) covalent geometry : angle 0.68228 (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 : 1.643 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 366 LEU cc_start: 0.8459 (tp) cc_final: 0.8132 (mp) REVERT: B 112 TYR cc_start: 0.8901 (m-80) cc_final: 0.8636 (m-80) REVERT: B 326 ASP cc_start: 0.7956 (m-30) cc_final: 0.7243 (p0) outliers start: 2 outliers final: 2 residues processed: 89 average time/residue: 0.5104 time to fit residues: 63.5517 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 : 1.618 ------------------------------------------------------------------------------- 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: 8.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 B 320 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.057335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.043422 restraints weight = 169700.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.045504 restraints weight = 79577.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.046989 restraints weight = 47433.490| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3505 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= 0.130 Angle : 0.685 13.617 14045 Z= 0.327 Chirality : 0.046 0.283 1616 Planarity : 0.004 0.047 1775 Dihedral : 7.677 55.395 2037 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -1.17 (0.23), residues: 1212 helix: -2.55 (0.49), residues: 82 sheet: -1.47 (0.39), residues: 137 loop : -0.52 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 474 HIS 0.007 0.001 HIS B 470 PHE 0.017 0.001 PHE B 173 TYR 0.009 0.001 TYR A 148 ARG 0.002 0.000 ARG C 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 13) link_NAG-ASN : angle 2.45585 ( 39) link_ALPHA1-6 : bond 0.00786 ( 2) link_ALPHA1-6 : angle 1.56922 ( 6) link_BETA1-4 : bond 0.01197 ( 18) link_BETA1-4 : angle 4.18644 ( 54) link_ALPHA1-3 : bond 0.01682 ( 2) link_ALPHA1-3 : angle 2.61013 ( 6) hydrogen bonds : bond 0.04302 ( 190) hydrogen bonds : angle 7.08995 ( 357) SS BOND : bond 0.00354 ( 51) SS BOND : angle 1.09454 ( 102) covalent geometry : bond 0.00279 (10202) covalent geometry : angle 0.61480 (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 79 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 1.587 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 218 ASP cc_start: 0.8634 (m-30) cc_final: 0.8336 (m-30) REVERT: A 366 LEU cc_start: 0.8523 (tp) cc_final: 0.8213 (mp) REVERT: B 326 ASP cc_start: 0.7919 (m-30) cc_final: 0.7221 (p0) outliers start: 2 outliers final: 2 residues processed: 79 average time/residue: 0.5725 time to fit residues: 62.2885 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 : 1.780 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.057231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.043252 restraints weight = 171200.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.045335 restraints weight = 78765.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.046816 restraints weight = 46786.645| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10288 Z= 0.120 Angle : 0.643 13.000 14045 Z= 0.309 Chirality : 0.045 0.275 1616 Planarity : 0.004 0.055 1775 Dihedral : 6.903 52.091 2037 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.11 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 (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: -1.04 (0.23), residues: 1212 helix: -2.20 (0.53), residues: 75 sheet: -1.47 (0.40), residues: 137 loop : -0.46 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.005 0.001 HIS B 470 PHE 0.013 0.001 PHE B 425 TYR 0.008 0.001 TYR A 148 ARG 0.002 0.000 ARG B 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 13) link_NAG-ASN : angle 2.20047 ( 39) link_ALPHA1-6 : bond 0.00790 ( 2) link_ALPHA1-6 : angle 1.52469 ( 6) link_BETA1-4 : bond 0.01167 ( 18) link_BETA1-4 : angle 3.88556 ( 54) link_ALPHA1-3 : bond 0.01724 ( 2) link_ALPHA1-3 : angle 2.87003 ( 6) hydrogen bonds : bond 0.03985 ( 190) hydrogen bonds : angle 6.88705 ( 357) SS BOND : bond 0.00323 ( 51) SS BOND : angle 0.98919 ( 102) covalent geometry : bond 0.00256 (10202) covalent geometry : angle 0.57945 (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 73 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 1.515 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 81 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6905 (mtt180) REVERT: A 366 LEU cc_start: 0.8427 (tp) cc_final: 0.8114 (mp) REVERT: B 326 ASP cc_start: 0.8052 (m-30) cc_final: 0.7312 (p0) outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.5608 time to fit residues: 56.0717 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 : 1.550 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 120 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 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 = 0.057530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.043547 restraints weight = 170913.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.045715 restraints weight = 77402.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.047195 restraints weight = 45179.266| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10288 Z= 0.094 Angle : 0.604 12.437 14045 Z= 0.290 Chirality : 0.045 0.267 1616 Planarity : 0.004 0.050 1775 Dihedral : 6.286 42.171 2037 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -1.00 (0.23), residues: 1212 helix: -2.25 (0.53), residues: 75 sheet: -1.31 (0.42), residues: 130 loop : -0.45 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.004 0.001 HIS B 470 PHE 0.010 0.001 PHE B 577 TYR 0.016 0.001 TYR B 411 ARG 0.002 0.000 ARG B 558 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 13) link_NAG-ASN : angle 1.97336 ( 39) link_ALPHA1-6 : bond 0.00814 ( 2) link_ALPHA1-6 : angle 1.45266 ( 6) link_BETA1-4 : bond 0.01157 ( 18) link_BETA1-4 : angle 3.65257 ( 54) link_ALPHA1-3 : bond 0.01779 ( 2) link_ALPHA1-3 : angle 3.08776 ( 6) hydrogen bonds : bond 0.03585 ( 190) hydrogen bonds : angle 6.61837 ( 357) SS BOND : bond 0.00283 ( 51) SS BOND : angle 0.92333 ( 102) covalent geometry : bond 0.00197 (10202) covalent geometry : angle 0.54401 (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 75 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 1.656 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 81 ARG cc_start: 0.7176 (mtm110) cc_final: 0.6923 (mtt180) REVERT: A 366 LEU cc_start: 0.8389 (tp) cc_final: 0.8103 (mp) REVERT: A 562 MET cc_start: 0.9554 (mmm) cc_final: 0.9296 (mmm) REVERT: B 326 ASP cc_start: 0.8012 (m-30) cc_final: 0.7314 (p0) outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.5630 time to fit residues: 57.8601 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 : 1.524 ------------------------------------------------------------------------------- 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: 0.7980 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.057152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.043183 restraints weight = 170147.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.045278 restraints weight = 77595.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.046743 restraints weight = 45688.889| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4115 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= 0.104 Angle : 0.593 11.812 14045 Z= 0.284 Chirality : 0.044 0.253 1616 Planarity : 0.004 0.053 1775 Dihedral : 5.903 40.793 2037 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: -1.00 (0.23), residues: 1212 helix: -2.18 (0.54), residues: 75 sheet: -1.37 (0.41), residues: 137 loop : -0.44 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 PHE 0.009 0.001 PHE B 577 TYR 0.007 0.001 TYR A 148 ARG 0.002 0.000 ARG C 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 13) link_NAG-ASN : angle 1.93803 ( 39) link_ALPHA1-6 : bond 0.00790 ( 2) link_ALPHA1-6 : angle 1.39414 ( 6) link_BETA1-4 : bond 0.01095 ( 18) link_BETA1-4 : angle 3.46666 ( 54) link_ALPHA1-3 : bond 0.01717 ( 2) link_ALPHA1-3 : angle 3.19792 ( 6) hydrogen bonds : bond 0.03425 ( 190) hydrogen bonds : angle 6.45987 ( 357) SS BOND : bond 0.00366 ( 51) SS BOND : angle 0.88025 ( 102) covalent geometry : bond 0.00222 (10202) covalent geometry : angle 0.53652 (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 74 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 1.711 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: 0.7129 (mtm110) cc_final: 0.6863 (mtt180) REVERT: A 366 LEU cc_start: 0.8437 (tp) cc_final: 0.8142 (mp) REVERT: A 562 MET cc_start: 0.9568 (mmm) cc_final: 0.9321 (mmm) REVERT: B 326 ASP cc_start: 0.7979 (m-30) cc_final: 0.7256 (p0) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.5543 time to fit residues: 56.3431 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 : 1.698 ------------------------------------------------------------------------------- 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: 0.0980 chunk 8 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 A 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.057017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.043130 restraints weight = 171117.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.045218 restraints weight = 77681.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.046664 restraints weight = 45670.489| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4279 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= 0.101 Angle : 0.584 11.634 14045 Z= 0.282 Chirality : 0.044 0.243 1616 Planarity : 0.004 0.049 1775 Dihedral : 5.772 39.264 2037 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -1.02 (0.24), residues: 1212 helix: -2.07 (0.55), residues: 75 sheet: -1.34 (0.42), residues: 130 loop : -0.48 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 PHE 0.016 0.001 PHE A 447 TYR 0.009 0.001 TYR B 83 ARG 0.002 0.000 ARG C 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 13) link_NAG-ASN : angle 1.86940 ( 39) link_ALPHA1-6 : bond 0.00767 ( 2) link_ALPHA1-6 : angle 1.38908 ( 6) link_BETA1-4 : bond 0.01085 ( 18) link_BETA1-4 : angle 3.38217 ( 54) link_ALPHA1-3 : bond 0.01632 ( 2) link_ALPHA1-3 : angle 3.16718 ( 6) hydrogen bonds : bond 0.03363 ( 190) hydrogen bonds : angle 6.39668 ( 357) SS BOND : bond 0.00288 ( 51) SS BOND : angle 0.92619 ( 102) covalent geometry : bond 0.00218 (10202) covalent geometry : angle 0.52977 (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 70 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.506 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: 0.8452 (tp) cc_final: 0.8140 (mp) REVERT: A 562 MET cc_start: 0.9580 (mmm) cc_final: 0.9331 (mmm) REVERT: B 326 ASP cc_start: 0.7999 (m-30) cc_final: 0.7260 (p0) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.5208 time to fit residues: 50.4851 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 : 1.531 ------------------------------------------------------------------------------- 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: 0.7980 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.056852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.042925 restraints weight = 170016.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.044983 restraints weight = 76978.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.046440 restraints weight = 45236.989| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10288 Z= 0.101 Angle : 0.578 11.147 14045 Z= 0.279 Chirality : 0.043 0.231 1616 Planarity : 0.004 0.043 1775 Dihedral : 5.609 41.477 2037 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.63 % 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: -1.01 (0.24), residues: 1212 helix: -2.02 (0.57), residues: 75 sheet: -1.32 (0.42), residues: 130 loop : -0.48 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 PHE 0.009 0.001 PHE B 400 TYR 0.006 0.001 TYR A 148 ARG 0.003 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 13) link_NAG-ASN : angle 1.87435 ( 39) link_ALPHA1-6 : bond 0.00740 ( 2) link_ALPHA1-6 : angle 1.38190 ( 6) link_BETA1-4 : bond 0.01043 ( 18) link_BETA1-4 : angle 3.24139 ( 54) link_ALPHA1-3 : bond 0.01584 ( 2) link_ALPHA1-3 : angle 3.12786 ( 6) hydrogen bonds : bond 0.03321 ( 190) hydrogen bonds : angle 6.31959 ( 357) SS BOND : bond 0.00287 ( 51) SS BOND : angle 0.85442 ( 102) covalent geometry : bond 0.00215 (10202) covalent geometry : angle 0.52728 (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 70 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.563 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: 0.8472 (tp) cc_final: 0.8167 (mp) REVERT: B 326 ASP cc_start: 0.8027 (m-30) cc_final: 0.7293 (p0) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.5392 time to fit residues: 52.5628 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 : 1.636 ------------------------------------------------------------------------------- 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: 0.7980 chunk 105 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.056730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.042819 restraints weight = 171147.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.044879 restraints weight = 78666.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.046292 restraints weight = 46537.042| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4606 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= 0.106 Angle : 0.572 10.928 14045 Z= 0.277 Chirality : 0.043 0.223 1616 Planarity : 0.004 0.041 1775 Dihedral : 5.566 42.555 2037 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % 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: -1.01 (0.24), residues: 1212 helix: -1.99 (0.58), residues: 75 sheet: -1.39 (0.42), residues: 137 loop : -0.46 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 PHE 0.014 0.001 PHE B 425 TYR 0.007 0.001 TYR B 83 ARG 0.002 0.000 ARG A 114 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 13) link_NAG-ASN : angle 1.84116 ( 39) link_ALPHA1-6 : bond 0.00708 ( 2) link_ALPHA1-6 : angle 1.38617 ( 6) link_BETA1-4 : bond 0.01040 ( 18) link_BETA1-4 : angle 3.18100 ( 54) link_ALPHA1-3 : bond 0.01489 ( 2) link_ALPHA1-3 : angle 3.02905 ( 6) hydrogen bonds : bond 0.03289 ( 190) hydrogen bonds : angle 6.23614 ( 357) SS BOND : bond 0.00284 ( 51) SS BOND : angle 1.00400 ( 102) covalent geometry : bond 0.00230 (10202) covalent geometry : angle 0.52012 (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 69 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 1.523 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: 0.8491 (tp) cc_final: 0.8179 (mp) REVERT: A 562 MET cc_start: 0.9576 (mmm) cc_final: 0.9341 (mmm) REVERT: B 326 ASP cc_start: 0.8035 (m-30) cc_final: 0.7283 (p0) outliers start: 2 outliers final: 2 residues processed: 69 average time/residue: 0.5358 time to fit residues: 51.0815 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 : 1.536 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.056932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.042956 restraints weight = 171493.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.045051 restraints weight = 78389.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.046511 restraints weight = 45920.969| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10288 Z= 0.085 Angle : 0.559 10.664 14045 Z= 0.268 Chirality : 0.043 0.218 1616 Planarity : 0.004 0.040 1775 Dihedral : 5.410 42.609 2037 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -0.96 (0.24), residues: 1212 helix: -1.93 (0.59), residues: 75 sheet: -1.14 (0.41), residues: 140 loop : -0.46 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.003 0.001 HIS B 267 PHE 0.009 0.001 PHE B 400 TYR 0.008 0.001 TYR A 148 ARG 0.003 0.000 ARG A 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 13) link_NAG-ASN : angle 1.75399 ( 39) link_ALPHA1-6 : bond 0.00680 ( 2) link_ALPHA1-6 : angle 1.39471 ( 6) link_BETA1-4 : bond 0.01037 ( 18) link_BETA1-4 : angle 3.10056 ( 54) link_ALPHA1-3 : bond 0.01466 ( 2) link_ALPHA1-3 : angle 2.94152 ( 6) hydrogen bonds : bond 0.02997 ( 190) hydrogen bonds : angle 6.14889 ( 357) SS BOND : bond 0.00230 ( 51) SS BOND : angle 0.81780 ( 102) covalent geometry : bond 0.00185 (10202) covalent geometry : angle 0.51135 (13838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6045.04 seconds wall clock time: 103 minutes 52.74 seconds (6232.74 seconds total)