Starting phenix.real_space_refine on Sun Dec 29 22:48:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t55_25695/12_2024/7t55_25695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t55_25695/12_2024/7t55_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_25695/12_2024/7t55_25695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t55_25695/12_2024/7t55_25695.map" model { file = "/net/cci-nas-00/data/ceres_data/7t55_25695/12_2024/7t55_25695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t55_25695/12_2024/7t55_25695.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.62, per 1000 atoms: 0.66 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: 2.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.14 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: 3.76 Time building geometry restraints manager: 3.35 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: 0.00 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: 4.670 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.900 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- 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= 0.240 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.018 0.002 TRP B 132 HIS 0.006 0.001 HIS B 207 PHE 0.016 0.001 PHE B 270 TYR 0.037 0.001 TYR B 389 ARG 0.016 0.001 ARG B 498 *********************** 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 : 1.270 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: 0.2497 time to fit residues: 69.5075 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 : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 0.0770 chunk 43 optimal weight: 0.4980 chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11636 Z= 0.179 Angle : 0.572 7.102 15696 Z= 0.304 Chirality : 0.042 0.166 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.964 77.744 1620 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.24 % Allowed : 3.45 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1456 helix: 1.53 (0.18), residues: 854 sheet: 0.23 (0.42), residues: 140 loop : -1.50 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 132 HIS 0.006 0.001 HIS B 207 PHE 0.018 0.001 PHE A 493 TYR 0.012 0.001 TYR B 33 ARG 0.007 0.001 ARG A 109 *********************** 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 142 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7304 (ttm) cc_final: 0.5173 (mtt) REVERT: A 528 LEU cc_start: 0.8063 (pt) cc_final: 0.7636 (tp) REVERT: B 25 CYS cc_start: 0.8103 (m) cc_final: 0.7746 (p) outliers start: 3 outliers final: 0 residues processed: 142 average time/residue: 0.2123 time to fit residues: 45.0781 Evaluate side-chains 92 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11636 Z= 0.251 Angle : 0.568 7.828 15696 Z= 0.304 Chirality : 0.041 0.191 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.829 86.863 1620 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.08 % Allowed : 4.09 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.22), residues: 1456 helix: 1.77 (0.19), residues: 840 sheet: 0.10 (0.41), residues: 140 loop : -1.27 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 718 HIS 0.004 0.001 HIS B 207 PHE 0.016 0.002 PHE B 493 TYR 0.011 0.001 TYR B 33 ARG 0.004 0.000 ARG A 109 *********************** 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 119 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.7889 (pt) cc_final: 0.7376 (tp) REVERT: B 25 CYS cc_start: 0.8135 (m) cc_final: 0.7779 (p) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2158 time to fit residues: 38.5109 Evaluate side-chains 87 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN B 602 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11636 Z= 0.182 Angle : 0.539 7.361 15696 Z= 0.285 Chirality : 0.041 0.201 1852 Planarity : 0.003 0.033 1944 Dihedral : 6.606 82.979 1620 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1456 helix: 1.90 (0.19), residues: 834 sheet: 0.30 (0.42), residues: 140 loop : -1.18 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 718 HIS 0.005 0.001 HIS B 207 PHE 0.012 0.001 PHE B 270 TYR 0.017 0.001 TYR B 714 ARG 0.002 0.000 ARG B 277 *********************** 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 119 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.7795 (pt) cc_final: 0.7335 (tp) REVERT: B 25 CYS cc_start: 0.8079 (m) cc_final: 0.7767 (p) REVERT: B 568 ASP cc_start: 0.8671 (t0) cc_final: 0.8437 (t0) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.2232 time to fit residues: 39.6827 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 : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 124 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 ASN B 51 GLN B 534 ASN B 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11636 Z= 0.176 Angle : 0.552 8.445 15696 Z= 0.290 Chirality : 0.041 0.156 1852 Planarity : 0.003 0.033 1944 Dihedral : 6.501 81.405 1620 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.08 % Allowed : 1.85 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1456 helix: 2.03 (0.19), residues: 824 sheet: 0.33 (0.43), residues: 140 loop : -1.18 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 718 HIS 0.004 0.001 HIS B 207 PHE 0.041 0.001 PHE B 173 TYR 0.011 0.001 TYR B 714 ARG 0.003 0.000 ARG A 14 *********************** 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 114 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.7808 (pt) cc_final: 0.7342 (tp) REVERT: B 568 ASP cc_start: 0.8672 (t0) cc_final: 0.8437 (t0) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2178 time to fit residues: 37.6150 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 : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 0.0270 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 0.0060 chunk 73 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3456 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= 0.146 Angle : 0.553 8.009 15696 Z= 0.287 Chirality : 0.041 0.244 1852 Planarity : 0.003 0.050 1944 Dihedral : 6.380 80.083 1620 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.23), residues: 1456 helix: 2.08 (0.19), residues: 826 sheet: 0.36 (0.43), residues: 140 loop : -1.17 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 PHE 0.012 0.001 PHE B 257 TYR 0.009 0.001 TYR B 714 ARG 0.012 0.000 ARG B 96 *********************** 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 117 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8472 (pp) cc_final: 0.7930 (pp) REVERT: A 528 LEU cc_start: 0.7947 (pt) cc_final: 0.7518 (tp) REVERT: B 25 CYS cc_start: 0.7916 (p) cc_final: 0.7552 (p) REVERT: B 236 MET cc_start: 0.7801 (tpp) cc_final: 0.7562 (tpp) REVERT: B 568 ASP cc_start: 0.8660 (t0) cc_final: 0.8428 (t0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2143 time to fit residues: 38.4363 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 : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11636 Z= 0.281 Angle : 0.619 7.055 15696 Z= 0.327 Chirality : 0.041 0.173 1852 Planarity : 0.003 0.040 1944 Dihedral : 6.528 77.690 1620 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.23), residues: 1456 helix: 2.04 (0.19), residues: 826 sheet: 0.16 (0.42), residues: 140 loop : -1.07 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 718 HIS 0.004 0.001 HIS A 660 PHE 0.018 0.002 PHE B 493 TYR 0.012 0.001 TYR B 714 ARG 0.006 0.000 ARG B 96 *********************** 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 108 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.7882 (pt) cc_final: 0.7282 (tp) REVERT: A 717 MET cc_start: 0.9186 (ptp) cc_final: 0.8700 (ptp) REVERT: B 25 CYS cc_start: 0.7898 (p) cc_final: 0.7538 (p) REVERT: B 568 ASP cc_start: 0.8788 (t0) cc_final: 0.8460 (t0) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2149 time to fit residues: 35.6089 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 : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 579 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11636 Z= 0.153 Angle : 0.564 7.427 15696 Z= 0.290 Chirality : 0.041 0.165 1852 Planarity : 0.002 0.033 1944 Dihedral : 6.361 78.955 1620 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1456 helix: 2.21 (0.19), residues: 826 sheet: 0.28 (0.42), residues: 140 loop : -1.11 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 PHE 0.010 0.001 PHE A 383 TYR 0.010 0.001 TYR B 33 ARG 0.005 0.000 ARG B 680 *********************** 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 113 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.7987 (ttm) cc_final: 0.7345 (mtt) REVERT: A 528 LEU cc_start: 0.7807 (pt) cc_final: 0.7297 (tp) REVERT: A 717 MET cc_start: 0.9191 (ptp) cc_final: 0.8698 (ptp) REVERT: B 25 CYS cc_start: 0.7871 (p) cc_final: 0.7483 (p) REVERT: B 568 ASP cc_start: 0.8771 (t0) cc_final: 0.8469 (t0) REVERT: B 717 MET cc_start: 0.9321 (pmm) cc_final: 0.8973 (pmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2275 time to fit residues: 38.1539 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 : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN A 579 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11636 Z= 0.167 Angle : 0.566 7.442 15696 Z= 0.292 Chirality : 0.042 0.314 1852 Planarity : 0.003 0.033 1944 Dihedral : 6.333 76.524 1620 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1456 helix: 2.20 (0.19), residues: 828 sheet: 0.36 (0.43), residues: 140 loop : -1.11 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 PHE 0.009 0.001 PHE A 213 TYR 0.010 0.001 TYR B 33 ARG 0.004 0.000 ARG A 14 *********************** 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 113 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 LEU cc_start: 0.8511 (pp) cc_final: 0.8100 (pp) REVERT: A 528 LEU cc_start: 0.7868 (pt) cc_final: 0.7329 (tp) REVERT: A 717 MET cc_start: 0.9189 (ptp) cc_final: 0.8691 (ptp) REVERT: B 25 CYS cc_start: 0.7896 (p) cc_final: 0.7524 (p) REVERT: B 568 ASP cc_start: 0.8732 (t0) cc_final: 0.8426 (t0) REVERT: B 717 MET cc_start: 0.9299 (pmm) cc_final: 0.8920 (pmm) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2275 time to fit residues: 38.5431 Evaluate side-chains 82 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11636 Z= 0.270 Angle : 0.637 7.920 15696 Z= 0.330 Chirality : 0.043 0.280 1852 Planarity : 0.003 0.046 1944 Dihedral : 6.548 76.040 1620 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1456 helix: 2.05 (0.19), residues: 830 sheet: 0.09 (0.43), residues: 138 loop : -1.07 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 718 HIS 0.004 0.001 HIS A 660 PHE 0.024 0.002 PHE A 173 TYR 0.012 0.001 TYR B 714 ARG 0.005 0.001 ARG A 14 ********************** 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 : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8190 (ppp) cc_final: 0.7747 (ppp) REVERT: A 288 MET cc_start: 0.7287 (ppp) cc_final: 0.6916 (ppp) REVERT: A 528 LEU cc_start: 0.8030 (pt) cc_final: 0.7332 (tp) REVERT: A 717 MET cc_start: 0.9240 (ptp) cc_final: 0.8700 (ptp) REVERT: B 25 CYS cc_start: 0.7947 (p) cc_final: 0.7311 (p) REVERT: B 37 MET cc_start: 0.8443 (tpp) cc_final: 0.8181 (mmm) REVERT: B 568 ASP cc_start: 0.8792 (t0) cc_final: 0.8506 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2066 time to fit residues: 31.7372 Evaluate side-chains 79 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.045464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.035853 restraints weight = 92960.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036867 restraints weight = 59414.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037595 restraints weight = 43388.103| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11636 Z= 0.227 Angle : 0.616 9.082 15696 Z= 0.317 Chirality : 0.042 0.275 1852 Planarity : 0.003 0.041 1944 Dihedral : 6.517 76.565 1620 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1456 helix: 2.11 (0.19), residues: 826 sheet: 0.07 (0.43), residues: 138 loop : -1.07 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 718 HIS 0.003 0.001 HIS B 207 PHE 0.020 0.002 PHE A 173 TYR 0.012 0.001 TYR B 33 ARG 0.010 0.001 ARG A 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1996.19 seconds wall clock time: 38 minutes 16.30 seconds (2296.30 seconds total)