Starting phenix.real_space_refine on Thu Mar 5 22:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oz8_71051/03_2026/9oz8_71051_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oz8_71051/03_2026/9oz8_71051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oz8_71051/03_2026/9oz8_71051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oz8_71051/03_2026/9oz8_71051.map" model { file = "/net/cci-nas-00/data/ceres_data/9oz8_71051/03_2026/9oz8_71051_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oz8_71051/03_2026/9oz8_71051_trim.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 212 5.16 5 C 7811 2.51 5 N 2262 2.21 5 O 2526 1.98 5 H 11731 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24542 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 11698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 11698 Classifications: {'peptide': 785} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 753} Chain breaks: 1 Chain: "C" Number of atoms: 11815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 11815 Classifications: {'peptide': 793} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 760} Chain: "A" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 903 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "D" 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: 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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 Time building chain proxies: 3.99, per 1000 atoms: 0.16 Number of scatterers: 24542 At special positions: 0 Unit cell: (123.57, 150.249, 188.163, 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 212 16.00 O 2526 8.00 N 2262 7.00 C 7811 6.00 H 11731 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=90, symmetry=0 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 231 " - pdb=" SG CYS A 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS C 270 " distance=2.04 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 330 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS B 407 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 444 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 451 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 468 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 552 " distance=2.03 Simple disulfide: pdb=" SG CYS B 559 " - pdb=" SG CYS B 572 " distance=2.03 Simple disulfide: pdb=" SG CYS B 566 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 600 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 628 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 640 " - pdb=" SG CYS B 665 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 688 " distance=2.03 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 692 " distance=2.03 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 724 " distance=2.03 Simple disulfide: pdb=" SG CYS B 719 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 752 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 760 " - pdb=" SG CYS B 805 " distance=2.03 Simple disulfide: pdb=" SG CYS B 773 " - pdb=" SG CYS B 799 " distance=2.03 Simple disulfide: pdb=" SG CYS B 794 " - pdb=" SG CYS B 812 " distance=2.03 Simple disulfide: pdb=" SG CYS B 797 " - pdb=" SG CYS B 806 " distance=2.03 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS C 268 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 330 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 356 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 395 " distance=2.03 Simple disulfide: pdb=" SG CYS C 401 " - pdb=" SG CYS C 413 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 438 " distance=2.03 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 451 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS C 480 " distance=2.03 Simple disulfide: pdb=" SG CYS C 486 " - pdb=" SG CYS C 499 " distance=2.03 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 508 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS C 521 " distance=2.03 Simple disulfide: pdb=" SG CYS C 525 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 541 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 552 " distance=2.03 Simple disulfide: pdb=" SG CYS C 559 " - pdb=" SG CYS C 572 " distance=2.03 Simple disulfide: pdb=" SG CYS C 566 " - pdb=" SG CYS C 581 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 613 " - pdb=" SG CYS C 628 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 640 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 688 " distance=2.03 Simple disulfide: pdb=" SG CYS C 663 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 677 " - pdb=" SG CYS C 689 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 692 " distance=2.03 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 724 " distance=2.03 Simple disulfide: pdb=" SG CYS C 719 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 752 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 760 " - pdb=" SG CYS C 805 " distance=2.03 Simple disulfide: pdb=" SG CYS C 773 " - pdb=" SG CYS C 799 " distance=2.03 Simple disulfide: pdb=" SG CYS C 794 " - pdb=" SG CYS C 812 " distance=2.03 Simple disulfide: pdb=" SG CYS C 797 " - pdb=" SG CYS C 806 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B2000 " - " ASN B 298 " " NAG B2001 " - " ASN B 293 " " NAG C 901 " - " ASN C 225 " " NAG C 902 " - " ASN C 293 " " NAG C 903 " - " ASN C 298 " " NAG C 904 " - " ASN C 53 " " NAG C 905 " - " ASN C 517 " " NAG D 1 " - " ASN B 225 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 716.9 milliseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3052 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 51 sheets defined 13.9% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 216 through 221 removed outlier: 4.307A pdb=" N GLN B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 267 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 604 through 609 Processing helix chain 'B' and resid 689 through 693 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 31 through 36 Processing helix chain 'C' and resid 70 through 80 removed outlier: 3.675A pdb=" N GLU C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE C 76 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 221 removed outlier: 4.113A pdb=" N SER C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 266 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 689 through 693 Processing helix chain 'C' and resid 695 through 699 removed outlier: 4.089A pdb=" N GLN C 699 " --> pdb=" O LEU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 762 Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'A' and resid 50 through 87 removed outlier: 3.568A pdb=" N ARG A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.630A pdb=" N ARG B 46 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.536A pdb=" N PHE B 87 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 156 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 172 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 166 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'B' and resid 136 through 137 removed outlier: 3.775A pdb=" N PHE B 104 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER B 118 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL B 102 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 276 removed outlier: 3.505A pdb=" N CYS B 274 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 320 Processing sheet with id=AA8, first strand: chain 'B' and resid 346 through 350 removed outlier: 3.890A pdb=" N LEU B 358 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 384 through 386 Processing sheet with id=AB1, first strand: chain 'B' and resid 411 through 415 Processing sheet with id=AB2, first strand: chain 'B' and resid 428 through 430 Processing sheet with id=AB3, first strand: chain 'B' and resid 455 through 460 Processing sheet with id=AB4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'B' and resid 497 through 502 Processing sheet with id=AB6, first strand: chain 'B' and resid 514 through 516 Processing sheet with id=AB7, first strand: chain 'B' and resid 534 through 535 Processing sheet with id=AB8, first strand: chain 'B' and resid 547 through 548 removed outlier: 3.610A pdb=" N THR B 554 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 570 through 572 Processing sheet with id=AC1, first strand: chain 'B' and resid 588 through 589 Processing sheet with id=AC2, first strand: chain 'B' and resid 619 through 620 Processing sheet with id=AC3, first strand: chain 'B' and resid 640 through 642 Processing sheet with id=AC4, first strand: chain 'B' and resid 652 through 654 Processing sheet with id=AC5, first strand: chain 'B' and resid 714 through 717 Processing sheet with id=AC6, first strand: chain 'B' and resid 754 through 755 Processing sheet with id=AC7, first strand: chain 'B' and resid 773 through 774 Processing sheet with id=AC8, first strand: chain 'B' and resid 786 through 788 Processing sheet with id=AC9, first strand: chain 'C' and resid 58 through 60 removed outlier: 4.437A pdb=" N VAL C 208 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU C 90 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 172 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 166 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LYS C 170 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 100 through 108 removed outlier: 6.906A pdb=" N LEU C 116 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER C 105 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU C 114 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS C 107 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 112 " --> pdb=" O HIS C 107 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR C 113 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 130 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 129 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 100 through 108 removed outlier: 6.906A pdb=" N LEU C 116 " --> pdb=" O ILE C 103 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER C 105 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU C 114 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS C 107 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 112 " --> pdb=" O HIS C 107 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N TYR C 113 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 130 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG C 130 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 274 through 276 Processing sheet with id=AD4, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.554A pdb=" N GLU C 304 " --> pdb=" O ASN C 293 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AD6, first strand: chain 'C' and resid 317 through 321 Processing sheet with id=AD7, first strand: chain 'C' and resid 358 through 362 removed outlier: 3.565A pdb=" N LEU C 358 " --> pdb=" O ILE C 369 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 384 through 386 Processing sheet with id=AD9, first strand: chain 'C' and resid 428 through 430 Processing sheet with id=AE1, first strand: chain 'C' and resid 455 through 460 Processing sheet with id=AE2, first strand: chain 'C' and resid 497 through 502 Processing sheet with id=AE3, first strand: chain 'C' and resid 515 through 516 Processing sheet with id=AE4, first strand: chain 'C' and resid 534 through 537 removed outlier: 4.894A pdb=" N CYS C 535 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA C 542 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 537 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 547 through 548 Processing sheet with id=AE6, first strand: chain 'C' and resid 570 through 573 removed outlier: 4.557A pdb=" N HIS C 580 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 587 through 589 Processing sheet with id=AE8, first strand: chain 'C' and resid 618 through 622 Processing sheet with id=AE9, first strand: chain 'C' and resid 639 through 642 Processing sheet with id=AF1, first strand: chain 'C' and resid 652 through 654 Processing sheet with id=AF2, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AF3, first strand: chain 'C' and resid 714 through 717 Processing sheet with id=AF4, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AF5, first strand: chain 'C' and resid 772 through 774 Processing sheet with id=AF6, first strand: chain 'C' and resid 786 through 788 removed outlier: 3.536A pdb=" N CYS C 805 " --> pdb=" O GLN C 798 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11730 1.03 - 1.23: 34 1.23 - 1.42: 5556 1.42 - 1.62: 7244 1.62 - 1.82: 243 Bond restraints: 24807 Sorted by residual: bond pdb=" N CYS B 636 " pdb=" H CYS B 636 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N VAL B 212 " pdb=" CA VAL B 212 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.42e+00 bond pdb=" C ALA C 159 " pdb=" O ALA C 159 " ideal model delta sigma weight residual 1.243 1.233 0.010 9.50e-03 1.11e+04 1.18e+00 bond pdb=" N ASP C 740 " pdb=" CA ASP C 740 " ideal model delta sigma weight residual 1.466 1.452 0.014 1.36e-02 5.41e+03 1.13e+00 bond pdb=" CA ILE C 307 " pdb=" CB ILE C 307 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.01e+00 ... (remaining 24802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 44542 7.10 - 14.20: 1 14.20 - 21.31: 0 21.31 - 28.41: 0 28.41 - 35.51: 6 Bond angle restraints: 44549 Sorted by residual: angle pdb=" C ILE C 556 " pdb=" CA ILE C 556 " pdb=" HA ILE C 556 " ideal model delta sigma weight residual 109.00 73.49 35.51 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C CYS C 535 " pdb=" CA CYS C 535 " pdb=" HA CYS C 535 " ideal model delta sigma weight residual 109.00 73.67 35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB ILE C 556 " pdb=" CA ILE C 556 " pdb=" HA ILE C 556 " ideal model delta sigma weight residual 109.00 74.00 35.00 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N CYS C 535 " pdb=" CA CYS C 535 " pdb=" HA CYS C 535 " ideal model delta sigma weight residual 110.00 75.24 34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N ILE C 556 " pdb=" CA ILE C 556 " pdb=" HA ILE C 556 " ideal model delta sigma weight residual 110.00 76.03 33.97 3.00e+00 1.11e-01 1.28e+02 ... (remaining 44544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 11307 16.18 - 32.36: 652 32.36 - 48.55: 180 48.55 - 64.73: 59 64.73 - 80.91: 6 Dihedral angle restraints: 12204 sinusoidal: 6702 harmonic: 5502 Sorted by residual: dihedral pdb=" CA LEU C 575 " pdb=" C LEU C 575 " pdb=" N PRO C 576 " pdb=" CA PRO C 576 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CB CYS C 444 " pdb=" SG CYS C 444 " pdb=" SG CYS C 457 " pdb=" CB CYS C 457 " ideal model delta sinusoidal sigma weight residual -86.00 -49.24 -36.76 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS B 583 " pdb=" SG CYS B 583 " pdb=" SG CYS B 600 " pdb=" CB CYS B 600 " ideal model delta sinusoidal sigma weight residual 93.00 128.60 -35.60 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1747 0.071 - 0.142: 174 0.142 - 0.213: 3 0.213 - 0.284: 2 0.284 - 0.355: 1 Chirality restraints: 1927 Sorted by residual: chirality pdb=" CA CYS C 535 " pdb=" N CYS C 535 " pdb=" C CYS C 535 " pdb=" CB CYS C 535 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA ILE C 556 " pdb=" N ILE C 556 " pdb=" C ILE C 556 " pdb=" CB ILE C 556 " both_signs ideal model delta sigma weight residual False 2.43 2.19 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 NAG C 905 " pdb=" ND2 ASN C 517 " pdb=" C2 NAG C 905 " pdb=" O5 NAG C 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1924 not shown) Planarity restraints: 3929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 178 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO B 179 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 693 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO C 694 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 694 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 694 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 369 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO B 370 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 370 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 370 " 0.019 5.00e-02 4.00e+02 ... (remaining 3926 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1607 2.22 - 2.82: 51618 2.82 - 3.41: 60547 3.41 - 4.01: 79635 4.01 - 4.60: 122688 Nonbonded interactions: 316095 Sorted by model distance: nonbonded pdb=" HA CYS C 535 " pdb=" HB2 CYS C 535 " model vdw 1.628 1.952 nonbonded pdb=" HA ILE C 556 " pdb=" HB ILE C 556 " model vdw 1.639 1.952 nonbonded pdb=" H CYS C 535 " pdb=" HA CYS C 535 " model vdw 1.682 1.816 nonbonded pdb=" H ILE C 556 " pdb=" HA ILE C 556 " model vdw 1.770 1.816 nonbonded pdb=" H TRP C 578 " pdb=" HD1 TRP C 578 " model vdw 1.850 2.100 ... (remaining 316090 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 'B' and (resid 24 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA o \ r name HB2 or name HB3 or name HD21)) or resid 54 through 516 or (resid 517 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or resid 518 th \ rough 2001)) selection = (chain 'C' and (resid 24 through 630 or resid 636 through 641 or (resid 642 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 643 through 813 or resid 904 through 90 \ 5)) } 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: 1.080 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: 0.140 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 21.450 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.003 0.022 13175 Z= 0.153 Angle : 0.588 10.412 17897 Z= 0.338 Chirality : 0.042 0.355 1927 Planarity : 0.003 0.034 2353 Dihedral : 10.241 80.912 4957 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.75 % Allowed : 4.32 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.21), residues: 1630 helix: 1.47 (0.40), residues: 189 sheet: -1.59 (0.30), residues: 267 loop : -0.50 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 112 TYR 0.009 0.001 TYR B 587 PHE 0.010 0.001 PHE B 217 TRP 0.008 0.001 TRP B 578 HIS 0.004 0.001 HIS B 491 Details of bonding type rmsd covalent geometry : bond 0.00296 (13076) covalent geometry : angle 0.57245 (17690) SS BOND : bond 0.00189 ( 90) SS BOND : angle 0.60226 ( 180) hydrogen bonds : bond 0.21324 ( 405) hydrogen bonds : angle 9.65180 ( 1041) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 4.75612 ( 3) link_NAG-ASN : bond 0.00339 ( 8) link_NAG-ASN : angle 3.25196 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.638 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: B 326 CYS cc_start: 0.5444 (OUTLIER) cc_final: 0.5147 (m) REVERT: C 276 MET cc_start: 0.8071 (tmm) cc_final: 0.7776 (tmm) REVERT: C 408 MET cc_start: 0.8485 (mmm) cc_final: 0.8208 (mmm) REVERT: C 506 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6929 (t-90) outliers start: 11 outliers final: 7 residues processed: 86 average time/residue: 0.2511 time to fit residues: 30.4144 Evaluate side-chains 59 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.087228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.065192 restraints weight = 163966.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.063117 restraints weight = 121563.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.063589 restraints weight = 94146.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.064254 restraints weight = 74900.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.064189 restraints weight = 65191.696| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13175 Z= 0.152 Angle : 0.567 9.095 17897 Z= 0.304 Chirality : 0.044 0.343 1927 Planarity : 0.005 0.106 2353 Dihedral : 5.453 25.545 1950 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.07 % Allowed : 1.44 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1630 helix: 1.52 (0.40), residues: 184 sheet: -1.44 (0.29), residues: 281 loop : -0.57 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 530 TYR 0.019 0.001 TYR B 321 PHE 0.023 0.001 PHE C 400 TRP 0.011 0.001 TRP C 732 HIS 0.009 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00329 (13076) covalent geometry : angle 0.54867 (17690) SS BOND : bond 0.00381 ( 90) SS BOND : angle 0.98960 ( 180) hydrogen bonds : bond 0.04598 ( 405) hydrogen bonds : angle 7.25247 ( 1041) link_BETA1-4 : bond 0.00070 ( 1) link_BETA1-4 : angle 4.01136 ( 3) link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 2.90476 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.605 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: C 207 ASP cc_start: 0.8609 (m-30) cc_final: 0.8061 (p0) REVERT: C 213 MET cc_start: 0.8780 (ptm) cc_final: 0.8528 (ptm) REVERT: C 262 MET cc_start: 0.8747 (ttp) cc_final: 0.7945 (ttp) REVERT: C 276 MET cc_start: 0.7935 (tmm) cc_final: 0.7730 (tmm) REVERT: C 408 MET cc_start: 0.8363 (mmm) cc_final: 0.8044 (mmm) outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.3110 time to fit residues: 24.5412 Evaluate side-chains 48 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 123 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.087206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.061652 restraints weight = 163637.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.060908 restraints weight = 92012.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061464 restraints weight = 74668.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.061546 restraints weight = 60873.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.061636 restraints weight = 58432.560| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13175 Z= 0.133 Angle : 0.533 9.022 17897 Z= 0.283 Chirality : 0.043 0.342 1927 Planarity : 0.004 0.124 2353 Dihedral : 5.333 25.687 1950 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.07 % Allowed : 1.17 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1630 helix: 1.74 (0.41), residues: 184 sheet: -1.25 (0.30), residues: 281 loop : -0.61 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 432 TYR 0.012 0.001 TYR B 587 PHE 0.012 0.001 PHE B 87 TRP 0.013 0.001 TRP C 732 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00284 (13076) covalent geometry : angle 0.51818 (17690) SS BOND : bond 0.00262 ( 90) SS BOND : angle 0.73565 ( 180) hydrogen bonds : bond 0.03932 ( 405) hydrogen bonds : angle 6.68806 ( 1041) link_BETA1-4 : bond 0.00243 ( 1) link_BETA1-4 : angle 3.95209 ( 3) link_NAG-ASN : bond 0.00257 ( 8) link_NAG-ASN : angle 2.80746 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.695 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: B 35 GLU cc_start: 0.8183 (tp30) cc_final: 0.7897 (tp30) REVERT: C 207 ASP cc_start: 0.8582 (m-30) cc_final: 0.8136 (p0) REVERT: C 220 GLN cc_start: 0.8238 (tt0) cc_final: 0.7394 (tp40) REVERT: C 262 MET cc_start: 0.8831 (ttp) cc_final: 0.8214 (ttp) REVERT: C 276 MET cc_start: 0.8012 (tmm) cc_final: 0.7790 (tmm) REVERT: C 408 MET cc_start: 0.8451 (mmm) cc_final: 0.8142 (mmm) REVERT: C 524 PHE cc_start: 0.7797 (t80) cc_final: 0.7586 (t80) outliers start: 1 outliers final: 1 residues processed: 58 average time/residue: 0.3163 time to fit residues: 25.1191 Evaluate side-chains 50 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 52 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.087347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.062290 restraints weight = 163439.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061947 restraints weight = 92499.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.061831 restraints weight = 67240.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062251 restraints weight = 65369.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.062221 restraints weight = 62766.399| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13175 Z= 0.109 Angle : 0.511 8.813 17897 Z= 0.270 Chirality : 0.043 0.341 1927 Planarity : 0.004 0.119 2353 Dihedral : 5.134 24.509 1950 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.07 % Allowed : 1.10 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1630 helix: 1.64 (0.40), residues: 191 sheet: -1.22 (0.30), residues: 281 loop : -0.62 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 85 TYR 0.013 0.001 TYR B 437 PHE 0.019 0.001 PHE B 593 TRP 0.010 0.001 TRP C 732 HIS 0.013 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00236 (13076) covalent geometry : angle 0.49626 (17690) SS BOND : bond 0.00325 ( 90) SS BOND : angle 0.73597 ( 180) hydrogen bonds : bond 0.03529 ( 405) hydrogen bonds : angle 6.35119 ( 1041) link_BETA1-4 : bond 0.00105 ( 1) link_BETA1-4 : angle 3.89758 ( 3) link_NAG-ASN : bond 0.00248 ( 8) link_NAG-ASN : angle 2.75466 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.511 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: B 35 GLU cc_start: 0.8077 (tp30) cc_final: 0.7824 (tp30) REVERT: C 207 ASP cc_start: 0.8561 (m-30) cc_final: 0.8125 (p0) REVERT: C 262 MET cc_start: 0.8828 (ttp) cc_final: 0.8349 (ttp) REVERT: C 408 MET cc_start: 0.8454 (mmm) cc_final: 0.8134 (mmm) REVERT: C 524 PHE cc_start: 0.7748 (t80) cc_final: 0.7529 (t80) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.3108 time to fit residues: 23.5181 Evaluate side-chains 49 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.086381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.060809 restraints weight = 163978.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.060211 restraints weight = 88804.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.060680 restraints weight = 73613.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060808 restraints weight = 67443.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060918 restraints weight = 60224.741| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13175 Z= 0.210 Angle : 0.571 9.004 17897 Z= 0.302 Chirality : 0.044 0.340 1927 Planarity : 0.004 0.044 2353 Dihedral : 5.506 29.630 1950 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.07 % Allowed : 1.58 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1630 helix: 1.58 (0.40), residues: 184 sheet: -1.37 (0.30), residues: 276 loop : -0.76 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 85 TYR 0.008 0.001 TYR B 437 PHE 0.015 0.002 PHE B 87 TRP 0.014 0.001 TRP C 732 HIS 0.009 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00453 (13076) covalent geometry : angle 0.55398 (17690) SS BOND : bond 0.00304 ( 90) SS BOND : angle 0.97297 ( 180) hydrogen bonds : bond 0.03770 ( 405) hydrogen bonds : angle 6.34055 ( 1041) link_BETA1-4 : bond 0.00347 ( 1) link_BETA1-4 : angle 4.31746 ( 3) link_NAG-ASN : bond 0.00357 ( 8) link_NAG-ASN : angle 2.70832 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.615 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: C 262 MET cc_start: 0.8888 (ttp) cc_final: 0.8346 (ttp) REVERT: C 408 MET cc_start: 0.8486 (mmm) cc_final: 0.8177 (mmm) REVERT: C 732 TRP cc_start: 0.8702 (p90) cc_final: 0.8116 (p90) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.2929 time to fit residues: 21.8249 Evaluate side-chains 47 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 72 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 139 optimal weight: 30.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.087145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061238 restraints weight = 163184.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061332 restraints weight = 88847.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.061454 restraints weight = 68186.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.061679 restraints weight = 62051.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.061753 restraints weight = 55962.833| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13175 Z= 0.101 Angle : 0.509 8.925 17897 Z= 0.268 Chirality : 0.043 0.338 1927 Planarity : 0.003 0.044 2353 Dihedral : 5.106 25.775 1950 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1630 helix: 1.69 (0.39), residues: 191 sheet: -1.31 (0.29), residues: 282 loop : -0.73 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.015 0.001 TYR B 587 PHE 0.012 0.001 PHE B 189 TRP 0.013 0.001 TRP C 732 HIS 0.006 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00220 (13076) covalent geometry : angle 0.49227 (17690) SS BOND : bond 0.00216 ( 90) SS BOND : angle 0.85381 ( 180) hydrogen bonds : bond 0.03304 ( 405) hydrogen bonds : angle 5.95085 ( 1041) link_BETA1-4 : bond 0.00259 ( 1) link_BETA1-4 : angle 3.90275 ( 3) link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 2.67097 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.616 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: C 262 MET cc_start: 0.8807 (ttp) cc_final: 0.8563 (ttp) REVERT: C 408 MET cc_start: 0.8452 (mmm) cc_final: 0.8126 (mmm) REVERT: C 671 MET cc_start: 0.6978 (tmm) cc_final: 0.6669 (tmm) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.2909 time to fit residues: 22.4073 Evaluate side-chains 48 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 153 optimal weight: 0.0470 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.086895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061304 restraints weight = 164349.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060561 restraints weight = 93019.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.061002 restraints weight = 84744.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061375 restraints weight = 64039.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061399 restraints weight = 58837.077| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13175 Z= 0.120 Angle : 0.502 8.568 17897 Z= 0.265 Chirality : 0.043 0.340 1927 Planarity : 0.003 0.036 2353 Dihedral : 5.031 29.883 1950 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.07 % Allowed : 0.75 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.21), residues: 1630 helix: 1.97 (0.40), residues: 184 sheet: -1.39 (0.29), residues: 284 loop : -0.69 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.017 0.001 TYR C 478 PHE 0.014 0.001 PHE B 563 TRP 0.014 0.001 TRP C 732 HIS 0.004 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00261 (13076) covalent geometry : angle 0.48675 (17690) SS BOND : bond 0.00214 ( 90) SS BOND : angle 0.78557 ( 180) hydrogen bonds : bond 0.03259 ( 405) hydrogen bonds : angle 5.82264 ( 1041) link_BETA1-4 : bond 0.00027 ( 1) link_BETA1-4 : angle 3.79451 ( 3) link_NAG-ASN : bond 0.00250 ( 8) link_NAG-ASN : angle 2.63788 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.710 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: C 262 MET cc_start: 0.8777 (ttp) cc_final: 0.8278 (ttp) REVERT: C 408 MET cc_start: 0.8449 (mmm) cc_final: 0.8134 (mmm) REVERT: C 671 MET cc_start: 0.6941 (tmm) cc_final: 0.6653 (tmm) outliers start: 1 outliers final: 1 residues processed: 53 average time/residue: 0.2775 time to fit residues: 21.1016 Evaluate side-chains 48 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.085712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.057615 restraints weight = 162489.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.058994 restraints weight = 91197.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059483 restraints weight = 68588.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.059831 restraints weight = 52716.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.059947 restraints weight = 49755.175| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13175 Z= 0.245 Angle : 0.591 8.826 17897 Z= 0.313 Chirality : 0.044 0.336 1927 Planarity : 0.004 0.048 2353 Dihedral : 5.547 31.554 1950 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.07 % Allowed : 0.55 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1630 helix: 1.57 (0.39), residues: 184 sheet: -1.58 (0.29), residues: 284 loop : -0.83 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 85 TYR 0.010 0.001 TYR B 626 PHE 0.019 0.002 PHE B 201 TRP 0.023 0.002 TRP C 732 HIS 0.005 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00527 (13076) covalent geometry : angle 0.57590 (17690) SS BOND : bond 0.00339 ( 90) SS BOND : angle 0.95245 ( 180) hydrogen bonds : bond 0.03724 ( 405) hydrogen bonds : angle 6.07569 ( 1041) link_BETA1-4 : bond 0.00457 ( 1) link_BETA1-4 : angle 4.40818 ( 3) link_NAG-ASN : bond 0.00377 ( 8) link_NAG-ASN : angle 2.67639 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.656 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: C 262 MET cc_start: 0.8859 (ttp) cc_final: 0.8453 (ttp) REVERT: C 408 MET cc_start: 0.8516 (mmm) cc_final: 0.8204 (mmm) REVERT: C 671 MET cc_start: 0.7050 (tmm) cc_final: 0.6768 (tmm) outliers start: 1 outliers final: 1 residues processed: 51 average time/residue: 0.2580 time to fit residues: 19.2734 Evaluate side-chains 46 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 41 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 132 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.086781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060951 restraints weight = 164505.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.061125 restraints weight = 105241.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061266 restraints weight = 69903.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061280 restraints weight = 68224.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061408 restraints weight = 62739.837| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13175 Z= 0.113 Angle : 0.517 9.107 17897 Z= 0.271 Chirality : 0.043 0.338 1927 Planarity : 0.004 0.054 2353 Dihedral : 5.204 28.686 1950 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1630 helix: 1.90 (0.40), residues: 184 sheet: -1.49 (0.29), residues: 278 loop : -0.74 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 754 TYR 0.010 0.001 TYR C 478 PHE 0.014 0.001 PHE B 563 TRP 0.014 0.001 TRP C 732 HIS 0.004 0.001 HIS C 611 Details of bonding type rmsd covalent geometry : bond 0.00248 (13076) covalent geometry : angle 0.50139 (17690) SS BOND : bond 0.00219 ( 90) SS BOND : angle 0.85400 ( 180) hydrogen bonds : bond 0.03297 ( 405) hydrogen bonds : angle 5.76810 ( 1041) link_BETA1-4 : bond 0.00036 ( 1) link_BETA1-4 : angle 4.05755 ( 3) link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 2.62014 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.683 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: C 262 MET cc_start: 0.8781 (ttp) cc_final: 0.8260 (ttp) REVERT: C 408 MET cc_start: 0.8340 (mmm) cc_final: 0.8031 (mmm) REVERT: C 671 MET cc_start: 0.6843 (tmm) cc_final: 0.6582 (tmm) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.2750 time to fit residues: 21.1171 Evaluate side-chains 47 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.087252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.061125 restraints weight = 162873.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.061765 restraints weight = 97279.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061874 restraints weight = 62993.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061858 restraints weight = 60457.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.061951 restraints weight = 58348.841| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13175 Z= 0.091 Angle : 0.495 8.400 17897 Z= 0.259 Chirality : 0.043 0.342 1927 Planarity : 0.003 0.041 2353 Dihedral : 4.828 24.743 1950 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.21), residues: 1630 helix: 2.15 (0.40), residues: 184 sheet: -1.39 (0.29), residues: 284 loop : -0.62 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 584 TYR 0.014 0.001 TYR B 587 PHE 0.010 0.001 PHE B 189 TRP 0.012 0.001 TRP C 732 HIS 0.004 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00201 (13076) covalent geometry : angle 0.48016 (17690) SS BOND : bond 0.00248 ( 90) SS BOND : angle 0.79837 ( 180) hydrogen bonds : bond 0.03039 ( 405) hydrogen bonds : angle 5.50335 ( 1041) link_BETA1-4 : bond 0.00267 ( 1) link_BETA1-4 : angle 3.50624 ( 3) link_NAG-ASN : bond 0.00243 ( 8) link_NAG-ASN : angle 2.57822 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.717 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: C 262 MET cc_start: 0.8723 (ttp) cc_final: 0.8242 (ttp) REVERT: C 408 MET cc_start: 0.8473 (mmm) cc_final: 0.8164 (mmm) REVERT: C 671 MET cc_start: 0.6909 (tmm) cc_final: 0.6667 (tmm) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.2452 time to fit residues: 19.7584 Evaluate side-chains 45 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.087301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060411 restraints weight = 163589.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061877 restraints weight = 87702.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061869 restraints weight = 59994.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.061983 restraints weight = 57594.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.062033 restraints weight = 53781.921| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13175 Z= 0.094 Angle : 0.488 8.142 17897 Z= 0.255 Chirality : 0.043 0.342 1927 Planarity : 0.003 0.039 2353 Dihedral : 4.734 24.822 1950 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.07 % Allowed : 0.07 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1630 helix: 2.24 (0.40), residues: 184 sheet: -1.31 (0.29), residues: 284 loop : -0.58 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 754 TYR 0.010 0.001 TYR B 587 PHE 0.009 0.001 PHE B 217 TRP 0.012 0.001 TRP C 732 HIS 0.003 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00209 (13076) covalent geometry : angle 0.47399 (17690) SS BOND : bond 0.00229 ( 90) SS BOND : angle 0.76600 ( 180) hydrogen bonds : bond 0.02972 ( 405) hydrogen bonds : angle 5.42005 ( 1041) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 3.41424 ( 3) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 2.52555 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.02 seconds wall clock time: 55 minutes 48.48 seconds (3348.48 seconds total)