Starting phenix.real_space_refine on Wed Mar 4 06:38:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t55_25695/03_2026/7t55_25695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t55_25695/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t55_25695/03_2026/7t55_25695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t55_25695/03_2026/7t55_25695.map" model { file = "/net/cci-nas-00/data/ceres_data/7t55_25695/03_2026/7t55_25695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t55_25695/03_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-5986/lib/python3.9/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: 0.90 Conformation dependent library (CDL) restraints added in 689.7 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: 0.37 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: 2.04 Time building geometry restraints manager: 1.23 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: 6377 17.04 - 34.07: 542 34.07 - 51.11: 120 51.11 - 68.14: 19 68.14 - 85.18: 10 Dihedral angle restraints: 7068 sinusoidal: 2846 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 7065 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: 2.560 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.210 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 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 : 13.628 85.179 4356 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 covalent geometry : bond 0.00368 (11636) covalent geometry : angle 0.71023 (15696) hydrogen bonds : bond 0.15749 ( 694) hydrogen bonds : angle 5.68102 ( 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 : 0.475 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: 0.0996 time to fit residues: 27.9511 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 : 0.414 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.048924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.038824 restraints weight = 87799.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.039882 restraints weight = 56662.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.040637 restraints weight = 41702.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041182 restraints weight = 33303.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041590 restraints weight = 28078.284| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11636 Z= 0.138 Angle : 0.569 7.063 15696 Z= 0.305 Chirality : 0.042 0.166 1852 Planarity : 0.003 0.035 1944 Dihedral : 7.010 78.671 1620 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.19 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: 0.20 (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 0.010 0.001 TRP B 132 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00282 (11636) covalent geometry : angle 0.56902 (15696) hydrogen bonds : bond 0.04882 ( 694) hydrogen bonds : angle 4.44300 ( 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 : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8774 (m-30) cc_final: 0.8418 (m-30) REVERT: A 99 HIS cc_start: 0.7927 (t-90) cc_final: 0.7673 (t-90) REVERT: A 154 MET cc_start: 0.9028 (mmm) cc_final: 0.8784 (mmm) REVERT: A 236 MET cc_start: 0.8199 (ttm) cc_final: 0.7002 (mtt) REVERT: A 288 MET cc_start: 0.9161 (ttt) cc_final: 0.8714 (ttt) REVERT: A 528 LEU cc_start: 0.9049 (pt) cc_final: 0.8487 (tp) REVERT: A 533 MET cc_start: 0.9128 (tpt) cc_final: 0.8843 (tpp) REVERT: B 88 ILE cc_start: 0.9340 (mt) cc_final: 0.9138 (mt) REVERT: B 136 LEU cc_start: 0.9255 (tt) cc_final: 0.9027 (pp) REVERT: B 193 LEU cc_start: 0.9580 (tp) cc_final: 0.9344 (tt) REVERT: B 379 MET cc_start: 0.8826 (mmp) cc_final: 0.8386 (mmm) REVERT: B 432 LEU cc_start: 0.9282 (mt) cc_final: 0.9002 (mt) outliers start: 3 outliers final: 0 residues processed: 135 average time/residue: 0.0850 time to fit residues: 17.6255 Evaluate side-chains 84 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 0.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3237 r_free = 0.3237 target = 0.048951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038963 restraints weight = 89882.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.040045 restraints weight = 57537.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.040827 restraints weight = 42016.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.041361 restraints weight = 33339.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.041777 restraints weight = 28285.910| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 11636 Z= 0.123 Angle : 0.525 8.735 15696 Z= 0.279 Chirality : 0.041 0.210 1852 Planarity : 0.003 0.033 1944 Dihedral : 6.747 86.801 1620 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % 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: 0.98 (0.23), residues: 1456 helix: 1.80 (0.19), residues: 842 sheet: 0.24 (0.42), residues: 140 loop : -1.34 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 109 TYR 0.014 0.001 TYR B 104 PHE 0.011 0.001 PHE A 493 TRP 0.007 0.001 TRP B 132 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00247 (11636) covalent geometry : angle 0.52541 (15696) hydrogen bonds : bond 0.04323 ( 694) hydrogen bonds : angle 4.23494 ( 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 124 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8773 (m-30) cc_final: 0.8433 (m-30) REVERT: A 99 HIS cc_start: 0.7864 (t-90) cc_final: 0.7488 (t-90) REVERT: A 154 MET cc_start: 0.9009 (mmm) cc_final: 0.8796 (mmm) REVERT: A 288 MET cc_start: 0.9122 (ttt) cc_final: 0.8633 (ttt) REVERT: A 387 MET cc_start: 0.9219 (mmt) cc_final: 0.8901 (mmm) REVERT: A 478 PHE cc_start: 0.8294 (m-80) cc_final: 0.8047 (m-80) REVERT: A 528 LEU cc_start: 0.9034 (pt) cc_final: 0.8495 (tp) REVERT: A 533 MET cc_start: 0.9133 (tpt) cc_final: 0.8869 (tpp) REVERT: B 25 CYS cc_start: 0.9306 (p) cc_final: 0.9014 (p) REVERT: B 432 LEU cc_start: 0.9299 (mt) cc_final: 0.9035 (mt) REVERT: B 568 ASP cc_start: 0.9492 (t70) cc_final: 0.9285 (t0) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.0837 time to fit residues: 15.8782 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 : 0.311 ------------------------------------------------------------------------------- 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: 0.0670 chunk 58 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 136 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.049242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039140 restraints weight = 88767.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040211 restraints weight = 57540.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.040991 restraints weight = 42195.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041542 restraints weight = 33605.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.041938 restraints weight = 28275.318| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2860 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= 0.114 Angle : 0.538 8.115 15696 Z= 0.280 Chirality : 0.041 0.156 1852 Planarity : 0.003 0.032 1944 Dihedral : 6.583 88.434 1620 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.16 % Allowed : 3.61 % Favored : 96.23 % 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: 1.06 (0.23), residues: 1456 helix: 1.84 (0.19), residues: 844 sheet: 0.42 (0.43), residues: 140 loop : -1.33 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.015 0.001 TYR B 714 PHE 0.011 0.001 PHE B 257 TRP 0.008 0.001 TRP A 132 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00216 (11636) covalent geometry : angle 0.53806 (15696) hydrogen bonds : bond 0.04006 ( 694) hydrogen bonds : angle 4.11210 ( 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 123 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8753 (m-30) cc_final: 0.8485 (m-30) REVERT: A 20 ASP cc_start: 0.8639 (t70) cc_final: 0.8295 (t0) REVERT: A 99 HIS cc_start: 0.7637 (t-90) cc_final: 0.7152 (t-90) REVERT: A 154 MET cc_start: 0.8948 (mmm) cc_final: 0.8748 (mmm) REVERT: A 223 LEU cc_start: 0.9441 (tp) cc_final: 0.9232 (tp) REVERT: A 236 MET cc_start: 0.8303 (ttm) cc_final: 0.6941 (mtt) REVERT: A 288 MET cc_start: 0.9061 (ttt) cc_final: 0.8816 (ttt) REVERT: A 478 PHE cc_start: 0.8328 (m-80) cc_final: 0.8062 (m-80) REVERT: A 528 LEU cc_start: 0.9015 (pt) cc_final: 0.8514 (tp) REVERT: B 16 TYR cc_start: 0.7848 (m-80) cc_final: 0.7257 (m-80) REVERT: B 25 CYS cc_start: 0.9290 (p) cc_final: 0.9009 (p) REVERT: B 193 LEU cc_start: 0.9555 (tp) cc_final: 0.9333 (tt) REVERT: B 379 MET cc_start: 0.8831 (mmp) cc_final: 0.8396 (mmt) REVERT: B 432 LEU cc_start: 0.9361 (mt) cc_final: 0.9078 (mt) REVERT: B 568 ASP cc_start: 0.9506 (t70) cc_final: 0.9292 (t0) outliers start: 2 outliers final: 0 residues processed: 123 average time/residue: 0.0825 time to fit residues: 15.8656 Evaluate side-chains 90 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 0.9990 chunk 126 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 132 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3198 r_free = 0.3198 target = 0.047189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037178 restraints weight = 90158.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038220 restraints weight = 57568.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038987 restraints weight = 41928.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.039522 restraints weight = 33199.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.039908 restraints weight = 27897.141| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3067 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= 0.172 Angle : 0.562 6.913 15696 Z= 0.299 Chirality : 0.041 0.239 1852 Planarity : 0.003 0.032 1944 Dihedral : 6.544 82.286 1620 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 1.20 (0.23), residues: 1456 helix: 1.95 (0.19), residues: 838 sheet: 0.40 (0.43), residues: 140 loop : -1.22 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.015 0.001 TYR A 56 PHE 0.013 0.001 PHE B 493 TRP 0.011 0.001 TRP B 718 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00360 (11636) covalent geometry : angle 0.56241 (15696) hydrogen bonds : bond 0.04078 ( 694) hydrogen bonds : angle 4.24962 ( 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 112 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8690 (m-30) cc_final: 0.8449 (m-30) REVERT: A 20 ASP cc_start: 0.8645 (t70) cc_final: 0.8172 (t0) REVERT: A 37 MET cc_start: 0.9029 (ptm) cc_final: 0.8193 (ppp) REVERT: A 99 HIS cc_start: 0.7910 (t-90) cc_final: 0.7427 (t-90) REVERT: A 288 MET cc_start: 0.9077 (ttt) cc_final: 0.8551 (ttt) REVERT: A 289 ILE cc_start: 0.8991 (mt) cc_final: 0.8729 (mt) REVERT: A 478 PHE cc_start: 0.8386 (m-80) cc_final: 0.8058 (m-80) REVERT: A 528 LEU cc_start: 0.9038 (pt) cc_final: 0.8476 (tp) REVERT: A 533 MET cc_start: 0.9133 (tpt) cc_final: 0.8845 (tpp) REVERT: B 16 TYR cc_start: 0.7887 (m-80) cc_final: 0.7172 (m-80) REVERT: B 88 ILE cc_start: 0.9444 (mt) cc_final: 0.9184 (mp) REVERT: B 432 LEU cc_start: 0.9402 (mt) cc_final: 0.9059 (mt) REVERT: B 568 ASP cc_start: 0.9509 (t70) cc_final: 0.9265 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0829 time to fit residues: 14.3473 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 : 0.372 ------------------------------------------------------------------------------- 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: 9.9990 chunk 53 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3213 r_free = 0.3213 target = 0.047562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.037553 restraints weight = 89947.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038601 restraints weight = 57727.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.039370 restraints weight = 42244.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.039907 restraints weight = 33519.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040297 restraints weight = 28164.777| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11636 Z= 0.120 Angle : 0.537 8.632 15696 Z= 0.280 Chirality : 0.040 0.161 1852 Planarity : 0.003 0.032 1944 Dihedral : 6.415 81.422 1620 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.08 % Allowed : 1.93 % Favored : 97.99 % 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: 1.31 (0.23), residues: 1456 helix: 2.10 (0.19), residues: 826 sheet: 0.41 (0.43), residues: 140 loop : -1.20 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.011 0.001 TYR A 714 PHE 0.012 0.001 PHE A 383 TRP 0.010 0.001 TRP B 718 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00246 (11636) covalent geometry : angle 0.53650 (15696) hydrogen bonds : bond 0.03936 ( 694) hydrogen bonds : angle 4.09502 ( 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 116 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8676 (m-30) cc_final: 0.7561 (m-30) REVERT: A 99 HIS cc_start: 0.8006 (t-90) cc_final: 0.7457 (t-90) REVERT: A 288 MET cc_start: 0.9016 (ttt) cc_final: 0.8503 (ttt) REVERT: A 289 ILE cc_start: 0.8921 (mt) cc_final: 0.8642 (mt) REVERT: A 478 PHE cc_start: 0.8384 (m-80) cc_final: 0.8026 (m-80) REVERT: A 528 LEU cc_start: 0.8959 (pt) cc_final: 0.8374 (tp) REVERT: A 533 MET cc_start: 0.9111 (tpt) cc_final: 0.8812 (tpp) REVERT: B 16 TYR cc_start: 0.7858 (m-80) cc_final: 0.7045 (m-80) REVERT: B 88 ILE cc_start: 0.9407 (mt) cc_final: 0.9149 (mp) REVERT: B 379 MET cc_start: 0.9012 (mmp) cc_final: 0.8456 (mmp) REVERT: B 432 LEU cc_start: 0.9428 (mt) cc_final: 0.9115 (mt) REVERT: B 568 ASP cc_start: 0.9497 (t70) cc_final: 0.9258 (t0) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.0783 time to fit residues: 14.2270 Evaluate side-chains 89 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3173 r_free = 0.3173 target = 0.046052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.036290 restraints weight = 89358.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.037281 restraints weight = 57543.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038027 restraints weight = 42093.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038554 restraints weight = 33366.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.038944 restraints weight = 27983.340| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11636 Z= 0.158 Angle : 0.566 7.458 15696 Z= 0.298 Chirality : 0.041 0.235 1852 Planarity : 0.003 0.032 1944 Dihedral : 6.443 79.090 1620 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 1.36 (0.23), residues: 1456 helix: 2.15 (0.19), residues: 824 sheet: 0.28 (0.42), residues: 140 loop : -1.12 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.013 0.001 TYR B 714 PHE 0.015 0.002 PHE B 326 TRP 0.013 0.001 TRP B 718 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00332 (11636) covalent geometry : angle 0.56600 (15696) hydrogen bonds : bond 0.04058 ( 694) hydrogen bonds : angle 4.22963 ( 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 109 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8886 (ptm) cc_final: 0.8229 (ppp) REVERT: A 99 HIS cc_start: 0.8042 (t-90) cc_final: 0.7561 (t-90) REVERT: A 236 MET cc_start: 0.9074 (mmp) cc_final: 0.8672 (tpp) REVERT: A 288 MET cc_start: 0.9098 (ttt) cc_final: 0.8805 (ttt) REVERT: A 478 PHE cc_start: 0.8416 (m-80) cc_final: 0.8005 (m-80) REVERT: A 528 LEU cc_start: 0.8958 (pt) cc_final: 0.8329 (tp) REVERT: A 533 MET cc_start: 0.9181 (tpt) cc_final: 0.8818 (tpp) REVERT: B 88 ILE cc_start: 0.9431 (mt) cc_final: 0.9174 (mp) REVERT: B 173 PHE cc_start: 0.9090 (t80) cc_final: 0.8821 (t80) REVERT: B 432 LEU cc_start: 0.9440 (mt) cc_final: 0.9104 (mt) REVERT: B 568 ASP cc_start: 0.9486 (t70) cc_final: 0.9251 (t0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0865 time to fit residues: 14.5583 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 : 0.358 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3219 r_free = 0.3219 target = 0.047546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037592 restraints weight = 89117.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.038645 restraints weight = 56724.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.039426 restraints weight = 41480.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039957 restraints weight = 32747.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040362 restraints weight = 27580.631| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3622 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= 0.112 Angle : 0.559 8.162 15696 Z= 0.287 Chirality : 0.041 0.209 1852 Planarity : 0.002 0.031 1944 Dihedral : 6.327 78.986 1620 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 1.42 (0.23), residues: 1456 helix: 2.21 (0.19), residues: 824 sheet: 0.37 (0.42), residues: 140 loop : -1.15 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 43 TYR 0.010 0.001 TYR B 714 PHE 0.011 0.001 PHE B 257 TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00227 (11636) covalent geometry : angle 0.55875 (15696) hydrogen bonds : bond 0.03869 ( 694) hydrogen bonds : angle 4.10804 ( 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 117 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8732 (ptm) cc_final: 0.7980 (ppp) REVERT: A 99 HIS cc_start: 0.7960 (t-90) cc_final: 0.7480 (t-90) REVERT: A 154 MET cc_start: 0.9004 (mmm) cc_final: 0.8803 (mmm) REVERT: A 218 LEU cc_start: 0.9750 (mm) cc_final: 0.9516 (tt) REVERT: A 236 MET cc_start: 0.8975 (mmp) cc_final: 0.8393 (mmt) REVERT: A 288 MET cc_start: 0.8964 (ttt) cc_final: 0.8467 (ttt) REVERT: A 289 ILE cc_start: 0.8940 (mt) cc_final: 0.8687 (mt) REVERT: A 387 MET cc_start: 0.9332 (mmt) cc_final: 0.8977 (mmm) REVERT: A 478 PHE cc_start: 0.8406 (m-80) cc_final: 0.8021 (m-80) REVERT: A 528 LEU cc_start: 0.8947 (pt) cc_final: 0.8339 (tp) REVERT: A 533 MET cc_start: 0.9155 (tpt) cc_final: 0.8839 (tpp) REVERT: B 16 TYR cc_start: 0.7893 (m-80) cc_final: 0.7056 (m-80) REVERT: B 88 ILE cc_start: 0.9389 (mt) cc_final: 0.9133 (mp) REVERT: B 379 MET cc_start: 0.8982 (mmp) cc_final: 0.8433 (tpp) REVERT: B 432 LEU cc_start: 0.9432 (mt) cc_final: 0.9107 (mt) REVERT: B 568 ASP cc_start: 0.9508 (t70) cc_final: 0.9266 (t0) REVERT: B 717 MET cc_start: 0.9540 (pmm) cc_final: 0.9221 (pmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0888 time to fit residues: 15.7071 Evaluate side-chains 91 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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: 9.9990 chunk 70 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 652 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035187 restraints weight = 94550.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036181 restraints weight = 60163.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036910 restraints weight = 43806.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037415 restraints weight = 34803.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037796 restraints weight = 29396.120| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11636 Z= 0.247 Angle : 0.685 7.027 15696 Z= 0.357 Chirality : 0.042 0.160 1852 Planarity : 0.003 0.052 1944 Dihedral : 6.677 77.625 1620 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 1.12 (0.22), residues: 1456 helix: 1.92 (0.19), residues: 826 sheet: 0.05 (0.41), residues: 140 loop : -1.11 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 14 TYR 0.017 0.002 TYR B 33 PHE 0.022 0.002 PHE B 326 TRP 0.020 0.002 TRP B 718 HIS 0.006 0.002 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00510 (11636) covalent geometry : angle 0.68485 (15696) hydrogen bonds : bond 0.04485 ( 694) hydrogen bonds : angle 4.60167 ( 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 100 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8788 (ptm) cc_final: 0.8324 (ppp) REVERT: A 218 LEU cc_start: 0.9736 (mm) cc_final: 0.9533 (tt) REVERT: A 236 MET cc_start: 0.8992 (mmp) cc_final: 0.8396 (mtt) REVERT: A 288 MET cc_start: 0.9198 (ttt) cc_final: 0.8876 (ttt) REVERT: A 478 PHE cc_start: 0.8456 (m-80) cc_final: 0.8011 (m-80) REVERT: A 528 LEU cc_start: 0.9090 (pt) cc_final: 0.8387 (tp) REVERT: A 533 MET cc_start: 0.9209 (tpt) cc_final: 0.8817 (tpp) REVERT: B 88 ILE cc_start: 0.9442 (mt) cc_final: 0.9186 (mp) REVERT: B 173 PHE cc_start: 0.9080 (t80) cc_final: 0.8868 (t80) REVERT: B 379 MET cc_start: 0.9101 (mmp) cc_final: 0.8118 (mmp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0850 time to fit residues: 13.1037 Evaluate side-chains 77 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 9.9990 chunk 137 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.045751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.036073 restraints weight = 93984.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037101 restraints weight = 60090.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.037847 restraints weight = 43638.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038376 restraints weight = 34621.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038769 restraints weight = 29124.700| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4015 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= 0.154 Angle : 0.603 10.757 15696 Z= 0.310 Chirality : 0.042 0.196 1852 Planarity : 0.003 0.030 1944 Dihedral : 6.560 77.218 1620 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: 1.29 (0.23), residues: 1456 helix: 2.08 (0.19), residues: 826 sheet: 0.04 (0.42), residues: 140 loop : -1.07 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 96 TYR 0.012 0.001 TYR B 714 PHE 0.014 0.001 PHE B 326 TRP 0.012 0.001 TRP A 132 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00325 (11636) covalent geometry : angle 0.60315 (15696) hydrogen bonds : bond 0.04176 ( 694) hydrogen bonds : angle 4.35817 ( 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 99 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8732 (ptm) cc_final: 0.7961 (ppp) REVERT: A 236 MET cc_start: 0.8964 (mmp) cc_final: 0.8327 (mtt) REVERT: A 288 MET cc_start: 0.9045 (ttt) cc_final: 0.8504 (ttt) REVERT: A 387 MET cc_start: 0.9329 (mmt) cc_final: 0.9057 (mmm) REVERT: A 478 PHE cc_start: 0.8515 (m-80) cc_final: 0.8062 (m-80) REVERT: A 528 LEU cc_start: 0.9033 (pt) cc_final: 0.8378 (tp) REVERT: A 533 MET cc_start: 0.9212 (tpt) cc_final: 0.8889 (tpp) REVERT: C 19 MET cc_start: 0.9328 (mmp) cc_final: 0.9077 (mmp) REVERT: B 88 ILE cc_start: 0.9451 (mt) cc_final: 0.9196 (mp) REVERT: B 379 MET cc_start: 0.9103 (mmp) cc_final: 0.8102 (mmm) REVERT: B 387 MET cc_start: 0.8821 (tmm) cc_final: 0.8604 (tmm) REVERT: B 432 LEU cc_start: 0.9435 (mt) cc_final: 0.9092 (mt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.0818 time to fit residues: 12.7334 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 : 0.308 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 62 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035907 restraints weight = 95203.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036920 restraints weight = 60404.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.037671 restraints weight = 43913.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038192 restraints weight = 34755.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.038585 restraints weight = 29267.084| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11636 Z= 0.153 Angle : 0.603 8.119 15696 Z= 0.311 Chirality : 0.042 0.193 1852 Planarity : 0.003 0.041 1944 Dihedral : 6.523 78.992 1620 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.33 (0.23), residues: 1456 helix: 2.10 (0.19), residues: 826 sheet: 0.03 (0.42), residues: 140 loop : -1.00 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.011 0.001 TYR B 33 PHE 0.014 0.001 PHE B 326 TRP 0.013 0.002 TRP B 718 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00321 (11636) covalent geometry : angle 0.60326 (15696) hydrogen bonds : bond 0.04108 ( 694) hydrogen bonds : angle 4.33399 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.09 seconds wall clock time: 26 minutes 47.10 seconds (1607.10 seconds total)