Starting phenix.real_space_refine on Fri Jul 3 02:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.map" model { file = "/net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t55_25695/07_2026/7t55_25695.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= 0.001 sd= 0.034 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 7382 2.51 5 N 1870 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11460 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5581 Classifications: {'peptide': 715} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 701} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 117 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.89, per 1000 atoms: 0.25 Number of scatterers: 11460 At special positions: 0 Unit cell: (106.09, 111.24, 139.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 2140 8.00 N 1870 7.00 C 7382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 463.2 milliseconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 63.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 removed outlier: 3.961A pdb=" N ALA A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 25 " --> pdb=" O CYS A 21 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.552A pdb=" N MET A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 125 through 132 removed outlier: 3.566A pdb=" N CYS A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.841A pdb=" N LYS A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 removed outlier: 4.151A pdb=" N PHE A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 202 through 252 removed outlier: 3.510A pdb=" N ILE A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 4.271A pdb=" N PHE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 305 removed outlier: 3.526A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 354 removed outlier: 4.939A pdb=" N LYS A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 3.502A pdb=" N SER A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 363 through 418 removed outlier: 3.563A pdb=" N THR A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.934A pdb=" N LEU A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 445 Proline residue: A 438 - end of helix Processing helix chain 'A' and resid 445 through 464 removed outlier: 4.086A pdb=" N VAL A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 560 Processing helix chain 'A' and resid 575 through 581 removed outlier: 4.159A pdb=" N CYS A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 removed outlier: 3.696A pdb=" N ILE A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.563A pdb=" N ILE A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 601 through 606' Processing helix chain 'A' and resid 624 through 640 removed outlier: 3.595A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 667 Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.645A pdb=" N LYS A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.677A pdb=" N CYS B 25 " --> pdb=" O CYS B 21 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 3.536A pdb=" N MET B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.546A pdb=" N PHE B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 131 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 removed outlier: 4.001A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 162 " --> pdb=" O PHE B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 188 removed outlier: 4.239A pdb=" N VAL B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.525A pdb=" N PHE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 251 removed outlier: 3.515A pdb=" N LEU B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 removed outlier: 4.171A pdb=" N PHE B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 305 removed outlier: 4.366A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 354 removed outlier: 3.774A pdb=" N PHE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.525A pdb=" N ALA B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 363 through 418 removed outlier: 3.568A pdb=" N SER B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 432 through 445 Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 445 through 465 removed outlier: 3.863A pdb=" N VAL B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.895A pdb=" N LEU B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 467 through 472' Processing helix chain 'B' and resid 526 through 533 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 576 through 580 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.670A pdb=" N ILE B 592 " --> pdb=" O ASP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 removed outlier: 3.644A pdb=" N PHE B 604 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 639 Processing helix chain 'B' and resid 653 through 668 removed outlier: 3.720A pdb=" N ASN B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 687 removed outlier: 3.676A pdb=" N VAL B 685 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 686 " --> pdb=" O THR B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 710 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.677A pdb=" N LYS B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 141 removed outlier: 3.659A pdb=" N ARG C 11 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 91 removed outlier: 3.744A pdb=" N VAL A 102 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR A 112 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A 106 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.860A pdb=" N ARG A 489 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP A 542 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 491 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS A 540 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 564 removed outlier: 3.659A pdb=" N ALA A 678 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 519 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N SER A 701 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 699 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 123 removed outlier: 6.873A pdb=" N ILE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE B 106 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 112 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 102 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG D 11 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 502 through 509 removed outlier: 7.155A pdb=" N LYS B 503 " --> pdb=" O ASP B 492 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 492 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE B 505 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN B 490 " --> pdb=" O ILE B 505 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N PHE B 488 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 544 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 490 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP B 542 " --> pdb=" O ASN B 490 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 540 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.796A pdb=" N GLY B 519 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 574 through 575 694 hydrogen bonds defined for protein. 2025 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: 1.84 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3620 1.34 - 1.46: 2119 1.46 - 1.58: 5783 1.58 - 1.70: 10 1.70 - 1.82: 104 Bond restraints: 11636 Sorted by residual: bond pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 1.579 1.604 -0.025 1.10e-02 8.26e+03 5.03e+00 bond pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 1.579 1.603 -0.024 1.10e-02 8.26e+03 4.62e+00 bond pdb=" O2B ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 1.529 1.490 0.039 2.20e-02 2.07e+03 3.20e+00 bond pdb=" O2A ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 1.529 1.491 0.038 2.20e-02 2.07e+03 2.95e+00 bond pdb=" O2B ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 1.529 1.491 0.038 2.20e-02 2.07e+03 2.92e+00 ... (remaining 11631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 15410 2.17 - 4.34: 235 4.34 - 6.51: 42 6.51 - 8.69: 8 8.69 - 10.86: 1 Bond angle restraints: 15696 Sorted by residual: angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 131.78 8.09 1.00e+00 1.00e+00 6.54e+01 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 131.82 8.05 1.00e+00 1.00e+00 6.49e+01 angle pdb=" C LYS A 640 " pdb=" N PRO A 641 " pdb=" CA PRO A 641 " ideal model delta sigma weight residual 119.85 126.17 -6.32 1.01e+00 9.80e-01 3.91e+01 angle pdb=" N ASP A 126 " pdb=" CA ASP A 126 " pdb=" C ASP A 126 " ideal model delta sigma weight residual 111.28 117.58 -6.30 1.09e+00 8.42e-01 3.34e+01 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 132.18 4.65 1.00e+00 1.00e+00 2.16e+01 ... (remaining 15691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 6355 17.04 - 34.07: 512 34.07 - 51.11: 114 51.11 - 68.14: 15 68.14 - 85.18: 10 Dihedral angle restraints: 7006 sinusoidal: 2784 harmonic: 4222 Sorted by residual: dihedral pdb=" CA LEU A 97 " pdb=" C LEU A 97 " pdb=" N ALA A 98 " pdb=" CA ALA A 98 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER B 130 " pdb=" C SER B 130 " pdb=" N ILE B 131 " pdb=" CA ILE B 131 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ILE B 480 " pdb=" C ILE B 480 " pdb=" N SER B 481 " pdb=" CA SER B 481 " ideal model delta harmonic sigma weight residual -180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1493 0.052 - 0.103: 296 0.103 - 0.155: 54 0.155 - 0.207: 6 0.207 - 0.259: 3 Chirality restraints: 1852 Sorted by residual: chirality pdb=" CG LEU B 308 " pdb=" CB LEU B 308 " pdb=" CD1 LEU B 308 " pdb=" CD2 LEU B 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE B 643 " pdb=" CA ILE B 643 " pdb=" CG1 ILE B 643 " pdb=" CG2 ILE B 643 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASP A 127 " pdb=" N ASP A 127 " pdb=" C ASP A 127 " pdb=" CB ASP A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1849 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 498 " 0.238 9.50e-02 1.11e+02 1.07e-01 7.79e+00 pdb=" NE ARG B 498 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 498 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 498 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 498 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 389 " -0.021 2.00e-02 2.50e+03 1.54e-02 4.72e+00 pdb=" CG TYR B 389 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 389 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 389 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 389 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 389 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 389 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 389 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 640 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 641 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.024 5.00e-02 4.00e+02 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 20 2.37 - 3.01: 6580 3.01 - 3.64: 17351 3.64 - 4.27: 23935 4.27 - 4.90: 39722 Nonbonded interactions: 87608 Sorted by model distance: nonbonded pdb=" O1B ATP B 801 " pdb="MG MG B 802 " model vdw 1.743 2.170 nonbonded pdb=" O2G ATP B 801 " pdb="MG MG B 802 " model vdw 2.029 2.170 nonbonded pdb=" O VAL B 11 " pdb=" OH TYR B 104 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLN A 336 " pdb=" OG SER A 381 " model vdw 2.237 3.040 nonbonded pdb=" CE2 TYR A 495 " pdb=" N1 ATP A 801 " model vdw 2.242 3.420 ... (remaining 87603 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11636 Z= 0.186 Angle : 0.710 10.856 15696 Z= 0.424 Chirality : 0.044 0.259 1852 Planarity : 0.004 0.107 1944 Dihedral : 13.291 85.179 4294 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.88 % Favored : 97.05 % Rotamer: Outliers : 0.24 % Allowed : 0.88 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.26 (0.22), residues: 1456 helix: 1.17 (0.18), residues: 830 sheet: -0.15 (0.42), residues: 142 loop : -1.45 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 498 TYR 0.037 0.001 TYR B 389 PHE 0.016 0.001 PHE B 270 TRP 0.018 0.002 TRP B 132 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (11636) covalent geometry : angle 0.71023 / 0.42 (15696) hydrogen bonds : bond 0.15749 / 10.33 ( 694) hydrogen bonds : angle 5.68102 / 3.99 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.7639 (tt) cc_final: 0.6613 (tt) REVERT: A 350 GLU cc_start: 0.7199 (tt0) cc_final: 0.5883 (tt0) REVERT: B 25 CYS cc_start: 0.8223 (m) cc_final: 0.7548 (p) REVERT: B 88 ILE cc_start: 0.8220 (mt) cc_final: 0.7786 (mt) REVERT: B 598 MET cc_start: 0.8289 (ptm) cc_final: 0.8059 (ttt) REVERT: D 19 MET cc_start: 0.7801 (mmm) cc_final: 0.7514 (mmm) outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.0966 time to fit residues: 27.2332 Evaluate side-chains 96 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 60 HIS A 579 ASN A 629 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 579 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.048920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038798 restraints weight = 87815.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039864 restraints weight = 56984.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040608 restraints weight = 41830.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041165 restraints weight = 33552.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041565 restraints weight = 28222.443| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11636 Z= 0.137 Angle : 0.568 7.022 15696 Z= 0.304 Chirality : 0.042 0.159 1852 Planarity : 0.003 0.035 1944 Dihedral : 5.054 72.048 1558 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.22), residues: 1456 helix: 1.57 (0.18), residues: 854 sheet: 0.19 (0.42), residues: 140 loop : -1.49 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 109 TYR 0.012 0.001 TYR B 33 PHE 0.017 0.001 PHE A 493 TRP 0.009 0.001 TRP B 132 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (11636) covalent geometry : angle 0.56837 / 0.30 (15696) hydrogen bonds : bond 0.04918 / 3.30 ( 694) hydrogen bonds : angle 4.44671 / 3.20 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8771 (m-30) cc_final: 0.8429 (m-30) REVERT: A 99 HIS cc_start: 0.7895 (t-90) cc_final: 0.7615 (t-90) REVERT: A 154 MET cc_start: 0.9017 (mmm) cc_final: 0.8779 (mmm) REVERT: A 236 MET cc_start: 0.8195 (ttm) cc_final: 0.6945 (mtt) REVERT: A 288 MET cc_start: 0.9132 (ttt) cc_final: 0.8673 (ttt) REVERT: A 528 LEU cc_start: 0.9042 (pt) cc_final: 0.8475 (tp) REVERT: A 533 MET cc_start: 0.9098 (tpt) cc_final: 0.8831 (tpp) REVERT: B 136 LEU cc_start: 0.9240 (tt) cc_final: 0.9017 (pp) REVERT: B 193 LEU cc_start: 0.9570 (tp) cc_final: 0.9332 (tt) REVERT: B 379 MET cc_start: 0.8818 (mmp) cc_final: 0.8374 (mmm) REVERT: B 432 LEU cc_start: 0.9286 (mt) cc_final: 0.9005 (mt) outliers start: 3 outliers final: 0 residues processed: 135 average time/residue: 0.0834 time to fit residues: 17.2501 Evaluate side-chains 83 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 579 ASN B 534 ASN B 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.046456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036201 restraints weight = 91902.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.037238 restraints weight = 58568.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.037996 restraints weight = 42756.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038534 restraints weight = 34024.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038912 restraints weight = 28719.009| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11636 Z= 0.201 Angle : 0.591 7.033 15696 Z= 0.316 Chirality : 0.041 0.179 1852 Planarity : 0.003 0.036 1944 Dihedral : 4.959 67.446 1558 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.08 % Allowed : 4.65 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.98 (0.23), residues: 1456 helix: 1.79 (0.19), residues: 840 sheet: 0.02 (0.41), residues: 140 loop : -1.25 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.014 0.001 TYR B 104 PHE 0.019 0.002 PHE B 493 TRP 0.010 0.001 TRP B 718 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (11636) covalent geometry : angle 0.59095 / 0.32 (15696) hydrogen bonds : bond 0.04660 / 3.15 ( 694) hydrogen bonds : angle 4.51464 / 3.23 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8748 (m-30) cc_final: 0.8444 (m-30) REVERT: A 20 ASP cc_start: 0.8646 (t0) cc_final: 0.8298 (t0) REVERT: A 288 MET cc_start: 0.9232 (ttt) cc_final: 0.8714 (ttt) REVERT: A 478 PHE cc_start: 0.8439 (m-80) cc_final: 0.8120 (m-80) REVERT: A 528 LEU cc_start: 0.9010 (pt) cc_final: 0.8344 (tp) REVERT: A 533 MET cc_start: 0.9303 (tpt) cc_final: 0.8840 (tpp) REVERT: B 25 CYS cc_start: 0.9345 (p) cc_final: 0.9008 (p) REVERT: B 432 LEU cc_start: 0.9308 (mt) cc_final: 0.8989 (mt) REVERT: B 568 ASP cc_start: 0.9508 (t70) cc_final: 0.9282 (t0) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0880 time to fit residues: 15.0294 Evaluate side-chains 86 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 136 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN B 534 ASN B 579 ASN B 602 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.046571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.036747 restraints weight = 88806.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037767 restraints weight = 57337.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.038497 restraints weight = 41963.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039024 restraints weight = 33441.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039423 restraints weight = 28128.413| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11636 Z= 0.123 Angle : 0.540 7.972 15696 Z= 0.281 Chirality : 0.041 0.212 1852 Planarity : 0.003 0.034 1944 Dihedral : 4.742 64.416 1558 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.08 % Allowed : 2.97 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.17 (0.23), residues: 1456 helix: 1.95 (0.19), residues: 836 sheet: 0.24 (0.42), residues: 140 loop : -1.21 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.011 0.001 TYR B 33 PHE 0.012 0.001 PHE B 257 TRP 0.007 0.001 TRP B 409 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (11636) covalent geometry : angle 0.54038 / 0.28 (15696) hydrogen bonds : bond 0.04264 / 2.86 ( 694) hydrogen bonds : angle 4.28651 / 3.07 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8794 (m-30) cc_final: 0.8473 (m-30) REVERT: A 99 HIS cc_start: 0.7979 (t-90) cc_final: 0.7510 (t-90) REVERT: A 236 MET cc_start: 0.8217 (ttm) cc_final: 0.6887 (mtt) REVERT: A 288 MET cc_start: 0.9154 (ttt) cc_final: 0.8666 (ttt) REVERT: A 289 ILE cc_start: 0.8994 (mt) cc_final: 0.8762 (mt) REVERT: A 478 PHE cc_start: 0.8383 (m-80) cc_final: 0.8047 (m-80) REVERT: A 528 LEU cc_start: 0.8918 (pt) cc_final: 0.8284 (tp) REVERT: A 533 MET cc_start: 0.9203 (tpt) cc_final: 0.8894 (tpp) REVERT: B 25 CYS cc_start: 0.9293 (p) cc_final: 0.8965 (p) REVERT: B 37 MET cc_start: 0.9035 (mmm) cc_final: 0.8504 (mpp) REVERT: B 173 PHE cc_start: 0.9104 (t80) cc_final: 0.8791 (t80) REVERT: B 288 MET cc_start: 0.8339 (mmt) cc_final: 0.8098 (mmt) REVERT: B 379 MET cc_start: 0.8863 (mmp) cc_final: 0.8391 (mmt) REVERT: B 432 LEU cc_start: 0.9380 (mt) cc_final: 0.9078 (mt) REVERT: B 568 ASP cc_start: 0.9501 (t70) cc_final: 0.9266 (t0) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.0902 time to fit residues: 15.4593 Evaluate side-chains 87 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN B 51 GLN B 534 ASN B 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.045309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035647 restraints weight = 89748.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036649 restraints weight = 57736.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037366 restraints weight = 42014.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.037886 restraints weight = 33297.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038251 restraints weight = 27993.034| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.160 Angle : 0.562 7.964 15696 Z= 0.296 Chirality : 0.041 0.155 1852 Planarity : 0.003 0.034 1944 Dihedral : 4.723 61.336 1558 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.32 (0.23), residues: 1456 helix: 2.07 (0.19), residues: 824 sheet: 0.21 (0.42), residues: 140 loop : -1.03 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 14 TYR 0.014 0.001 TYR A 56 PHE 0.015 0.001 PHE B 493 TRP 0.009 0.001 TRP B 718 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (11636) covalent geometry : angle 0.56209 / 0.30 (15696) hydrogen bonds : bond 0.04228 / 2.87 ( 694) hydrogen bonds : angle 4.31002 / 3.08 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8722 (m-30) cc_final: 0.8461 (m-30) REVERT: A 37 MET cc_start: 0.8922 (ptm) cc_final: 0.8171 (ppp) REVERT: A 99 HIS cc_start: 0.8202 (t-90) cc_final: 0.7731 (t-90) REVERT: A 288 MET cc_start: 0.9115 (ttt) cc_final: 0.8642 (ttt) REVERT: A 478 PHE cc_start: 0.8429 (m-80) cc_final: 0.8034 (m-80) REVERT: A 528 LEU cc_start: 0.8974 (pt) cc_final: 0.8325 (tp) REVERT: A 533 MET cc_start: 0.9206 (tpt) cc_final: 0.8872 (tpp) REVERT: A 717 MET cc_start: 0.9379 (ptp) cc_final: 0.9073 (ptp) REVERT: C 19 MET cc_start: 0.9433 (mmp) cc_final: 0.9204 (mmm) REVERT: B 37 MET cc_start: 0.9122 (mmm) cc_final: 0.8497 (mpp) REVERT: B 88 ILE cc_start: 0.9446 (mt) cc_final: 0.9182 (mp) REVERT: B 173 PHE cc_start: 0.9124 (t80) cc_final: 0.8832 (t80) REVERT: B 288 MET cc_start: 0.8351 (mmt) cc_final: 0.8092 (mmt) REVERT: B 432 LEU cc_start: 0.9405 (mt) cc_final: 0.9067 (mt) REVERT: B 568 ASP cc_start: 0.9471 (t70) cc_final: 0.9232 (t0) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0821 time to fit residues: 14.0000 Evaluate side-chains 81 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 534 ASN B 579 ASN B 652 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.036375 restraints weight = 92743.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.037421 restraints weight = 58730.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038176 restraints weight = 42682.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038690 restraints weight = 33843.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.039078 restraints weight = 28568.432| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11636 Z= 0.144 Angle : 0.553 7.362 15696 Z= 0.288 Chirality : 0.041 0.231 1852 Planarity : 0.003 0.061 1944 Dihedral : 4.702 60.646 1558 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.32 (0.23), residues: 1456 helix: 2.10 (0.19), residues: 826 sheet: 0.18 (0.41), residues: 140 loop : -1.09 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 96 TYR 0.010 0.001 TYR B 33 PHE 0.012 0.001 PHE B 428 TRP 0.009 0.001 TRP A 132 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11636) covalent geometry : angle 0.55266 / 0.29 (15696) hydrogen bonds : bond 0.04104 / 2.76 ( 694) hydrogen bonds : angle 4.22262 / 3.01 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8922 (ptm) cc_final: 0.8175 (ppp) REVERT: A 99 HIS cc_start: 0.8308 (t-90) cc_final: 0.7843 (t-90) REVERT: A 288 MET cc_start: 0.9169 (ttt) cc_final: 0.8886 (ttt) REVERT: A 387 MET cc_start: 0.9372 (mmt) cc_final: 0.8975 (mmm) REVERT: A 478 PHE cc_start: 0.8437 (m-80) cc_final: 0.8082 (m-80) REVERT: A 528 LEU cc_start: 0.8983 (pt) cc_final: 0.8341 (tp) REVERT: A 533 MET cc_start: 0.9203 (tpt) cc_final: 0.8874 (tpp) REVERT: B 37 MET cc_start: 0.9139 (mmm) cc_final: 0.8532 (mpp) REVERT: B 88 ILE cc_start: 0.9410 (mt) cc_final: 0.9147 (mp) REVERT: B 173 PHE cc_start: 0.9123 (t80) cc_final: 0.8761 (t80) REVERT: B 288 MET cc_start: 0.8339 (mmt) cc_final: 0.8065 (mmt) REVERT: B 379 MET cc_start: 0.9101 (mmp) cc_final: 0.8141 (mmp) REVERT: B 432 LEU cc_start: 0.9447 (mt) cc_final: 0.9121 (mt) REVERT: B 568 ASP cc_start: 0.9476 (t70) cc_final: 0.9242 (t0) REVERT: B 613 ASP cc_start: 0.8283 (p0) cc_final: 0.7691 (p0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0814 time to fit residues: 13.8238 Evaluate side-chains 80 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 534 ASN B 579 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.036748 restraints weight = 89775.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037803 restraints weight = 56717.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038573 restraints weight = 41398.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039112 restraints weight = 32802.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.039513 restraints weight = 27551.355| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11636 Z= 0.110 Angle : 0.543 7.481 15696 Z= 0.278 Chirality : 0.041 0.180 1852 Planarity : 0.003 0.043 1944 Dihedral : 4.587 60.164 1558 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.44 (0.23), residues: 1456 helix: 2.24 (0.19), residues: 824 sheet: 0.23 (0.41), residues: 140 loop : -1.11 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 680 TYR 0.013 0.001 TYR B 612 PHE 0.009 0.001 PHE B 604 TRP 0.010 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (11636) covalent geometry : angle 0.54278 / 0.28 (15696) hydrogen bonds : bond 0.03871 / 2.60 ( 694) hydrogen bonds : angle 4.03680 / 2.88 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8273 (t-90) cc_final: 0.7755 (t-90) REVERT: A 236 MET cc_start: 0.8812 (tpp) cc_final: 0.7948 (tpp) REVERT: A 288 MET cc_start: 0.9116 (ttt) cc_final: 0.8824 (ttt) REVERT: A 478 PHE cc_start: 0.8441 (m-80) cc_final: 0.8016 (m-80) REVERT: A 528 LEU cc_start: 0.8931 (pt) cc_final: 0.8305 (tp) REVERT: A 533 MET cc_start: 0.9169 (tpt) cc_final: 0.8869 (tpp) REVERT: B 16 TYR cc_start: 0.7907 (m-80) cc_final: 0.7031 (m-80) REVERT: B 37 MET cc_start: 0.9161 (mmm) cc_final: 0.8560 (mpp) REVERT: B 88 ILE cc_start: 0.9408 (mt) cc_final: 0.9147 (mp) REVERT: B 173 PHE cc_start: 0.9089 (t80) cc_final: 0.8723 (t80) REVERT: B 288 MET cc_start: 0.8290 (mmt) cc_final: 0.7996 (mmt) REVERT: B 379 MET cc_start: 0.8965 (mmp) cc_final: 0.8654 (mmp) REVERT: B 432 LEU cc_start: 0.9445 (mt) cc_final: 0.9123 (mt) REVERT: B 568 ASP cc_start: 0.9480 (t70) cc_final: 0.9246 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0838 time to fit residues: 14.5815 Evaluate side-chains 85 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 36 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 579 ASN B 534 ASN B 579 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.046840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036996 restraints weight = 89406.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038059 restraints weight = 56836.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038816 restraints weight = 41316.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.039347 restraints weight = 32921.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.039734 restraints weight = 27740.043| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11636 Z= 0.110 Angle : 0.549 8.186 15696 Z= 0.279 Chirality : 0.041 0.157 1852 Planarity : 0.003 0.035 1944 Dihedral : 4.526 58.421 1558 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.51 (0.23), residues: 1456 helix: 2.29 (0.19), residues: 824 sheet: 0.30 (0.42), residues: 140 loop : -1.07 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 14 TYR 0.009 0.001 TYR B 714 PHE 0.010 0.001 PHE B 604 TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (11636) covalent geometry : angle 0.54891 / 0.28 (15696) hydrogen bonds : bond 0.03728 / 2.52 ( 694) hydrogen bonds : angle 4.04390 / 2.86 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8219 (t-90) cc_final: 0.7871 (t-90) REVERT: A 154 MET cc_start: 0.8969 (mmm) cc_final: 0.8714 (mmm) REVERT: A 236 MET cc_start: 0.8760 (tpp) cc_final: 0.6858 (tpp) REVERT: A 288 MET cc_start: 0.9121 (ttt) cc_final: 0.8786 (ttt) REVERT: A 387 MET cc_start: 0.9317 (mmt) cc_final: 0.8957 (mmm) REVERT: A 478 PHE cc_start: 0.8453 (m-80) cc_final: 0.8019 (m-80) REVERT: A 528 LEU cc_start: 0.8949 (pt) cc_final: 0.8367 (tp) REVERT: A 533 MET cc_start: 0.9157 (tpt) cc_final: 0.8922 (tpp) REVERT: B 16 TYR cc_start: 0.7833 (m-80) cc_final: 0.7091 (m-80) REVERT: B 37 MET cc_start: 0.9174 (mmm) cc_final: 0.8561 (mpp) REVERT: B 88 ILE cc_start: 0.9392 (mt) cc_final: 0.9141 (mp) REVERT: B 173 PHE cc_start: 0.9099 (t80) cc_final: 0.8870 (t80) REVERT: B 288 MET cc_start: 0.8277 (mmt) cc_final: 0.8065 (mmt) REVERT: B 379 MET cc_start: 0.8943 (mmp) cc_final: 0.8326 (mmt) REVERT: B 432 LEU cc_start: 0.9458 (mt) cc_final: 0.9139 (mt) REVERT: B 568 ASP cc_start: 0.9483 (t70) cc_final: 0.9256 (t0) REVERT: B 613 ASP cc_start: 0.8283 (p0) cc_final: 0.8000 (p0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0952 time to fit residues: 16.2789 Evaluate side-chains 92 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN ** B 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.044360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034850 restraints weight = 96231.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035815 restraints weight = 61456.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036528 restraints weight = 45187.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037022 restraints weight = 36076.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037385 restraints weight = 30521.582| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11636 Z= 0.305 Angle : 0.704 12.651 15696 Z= 0.367 Chirality : 0.043 0.320 1852 Planarity : 0.003 0.065 1944 Dihedral : 4.916 64.138 1558 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.17 (0.23), residues: 1456 helix: 1.95 (0.19), residues: 826 sheet: 0.02 (0.41), residues: 140 loop : -1.06 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 14 TYR 0.022 0.002 TYR B 612 PHE 0.025 0.002 PHE B 326 TRP 0.015 0.002 TRP B 718 HIS 0.006 0.002 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.30 (11636) covalent geometry : angle 0.70370 / 0.37 (15696) hydrogen bonds : bond 0.04327 / 2.94 ( 694) hydrogen bonds : angle 4.65220 / 3.29 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8576 (t-90) cc_final: 0.8270 (t-90) REVERT: A 236 MET cc_start: 0.8882 (tpp) cc_final: 0.7346 (mmm) REVERT: A 288 MET cc_start: 0.9218 (ttt) cc_final: 0.8769 (ttt) REVERT: A 478 PHE cc_start: 0.8578 (m-80) cc_final: 0.8108 (m-80) REVERT: A 528 LEU cc_start: 0.9128 (pt) cc_final: 0.8448 (tp) REVERT: A 533 MET cc_start: 0.9279 (tpt) cc_final: 0.8921 (tpp) REVERT: B 88 ILE cc_start: 0.9460 (mt) cc_final: 0.9204 (mp) REVERT: B 379 MET cc_start: 0.9060 (mmp) cc_final: 0.8330 (mmp) REVERT: B 568 ASP cc_start: 0.9468 (t70) cc_final: 0.9266 (t0) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0871 time to fit residues: 13.8520 Evaluate side-chains 78 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.044438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034800 restraints weight = 93369.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035802 restraints weight = 59540.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.036524 restraints weight = 43322.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.037008 restraints weight = 34454.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037385 restraints weight = 29213.332| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11636 Z= 0.184 Angle : 0.616 8.482 15696 Z= 0.318 Chirality : 0.042 0.317 1852 Planarity : 0.003 0.042 1944 Dihedral : 4.950 67.501 1558 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.25 (0.23), residues: 1456 helix: 2.01 (0.19), residues: 826 sheet: 0.03 (0.42), residues: 140 loop : -1.01 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 96 TYR 0.017 0.001 TYR B 714 PHE 0.019 0.002 PHE B 326 TRP 0.012 0.002 TRP B 718 HIS 0.003 0.001 HIS B 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (11636) covalent geometry : angle 0.61621 / 0.32 (15696) hydrogen bonds : bond 0.04258 / 2.87 ( 694) hydrogen bonds : angle 4.46312 / 3.16 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8693 (t-90) cc_final: 0.8365 (t-90) REVERT: A 236 MET cc_start: 0.8781 (tpp) cc_final: 0.7907 (tpp) REVERT: A 288 MET cc_start: 0.9186 (ttt) cc_final: 0.8733 (ttt) REVERT: A 528 LEU cc_start: 0.9092 (pt) cc_final: 0.8420 (tp) REVERT: A 533 MET cc_start: 0.9233 (tpt) cc_final: 0.8892 (tpp) REVERT: B 88 ILE cc_start: 0.9454 (mt) cc_final: 0.9200 (mp) REVERT: B 432 LEU cc_start: 0.9459 (mt) cc_final: 0.9108 (mt) REVERT: B 568 ASP cc_start: 0.9477 (t70) cc_final: 0.9277 (t0) REVERT: B 613 ASP cc_start: 0.8700 (m-30) cc_final: 0.8499 (m-30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0859 time to fit residues: 13.9847 Evaluate side-chains 81 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.044199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034563 restraints weight = 94701.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035567 restraints weight = 60201.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.036282 restraints weight = 43814.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.036765 restraints weight = 34759.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037153 restraints weight = 29409.965| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11636 Z= 0.192 Angle : 0.622 8.246 15696 Z= 0.323 Chirality : 0.042 0.284 1852 Planarity : 0.003 0.045 1944 Dihedral : 5.014 68.346 1558 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.19 (0.23), residues: 1456 helix: 1.97 (0.19), residues: 824 sheet: -0.08 (0.43), residues: 138 loop : -1.00 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 96 TYR 0.015 0.001 TYR B 33 PHE 0.019 0.002 PHE B 326 TRP 0.015 0.002 TRP B 718 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (11636) covalent geometry : angle 0.62220 / 0.32 (15696) hydrogen bonds : bond 0.04338 / 2.93 ( 694) hydrogen bonds : angle 4.52789 / 3.19 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1556.19 seconds wall clock time: 28 minutes 4.70 seconds (1684.70 seconds total)