Starting phenix.real_space_refine on Tue Jun 10 11:03:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t55_25695/06_2025/7t55_25695.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t55_25695/06_2025/7t55_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_25695/06_2025/7t55_25695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t55_25695/06_2025/7t55_25695.map" model { file = "/net/cci-nas-00/data/ceres_data/7t55_25695/06_2025/7t55_25695.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t55_25695/06_2025/7t55_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.96, per 1000 atoms: 1.39 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: 5.09 Conformation dependent library (CDL) restraints added in 1.7 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: 1.55 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: 4.76 Time building geometry restraints manager: 5.66 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: 0.06 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: 65.750 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: 0.090 Extract box with map and model: 0.730 Check model and map are aligned: 0.210 Set scattering table: 0.340 Process input model: 49.900 Find NCS groups from input model: 1.010 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.340 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15749 ( 694) hydrogen bonds : angle 5.68102 ( 2025) covalent geometry : bond 0.00368 (11636) covalent geometry : angle 0.71023 (15696) *********************** 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 : 1.334 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: 0.2423 time to fit residues: 67.5173 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 : 1.330 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.049747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039772 restraints weight = 87430.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.040845 restraints weight = 56783.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.041604 restraints weight = 41920.875| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1999 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= 0.134 Angle : 0.572 7.103 15696 Z= 0.304 Chirality : 0.042 0.166 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.964 77.737 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 : 3.37 % 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 694) hydrogen bonds : angle 4.39269 ( 2025) covalent geometry : bond 0.00269 (11636) covalent geometry : angle 0.57151 (15696) *********************** 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 : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8871 (m-30) cc_final: 0.8527 (m-30) REVERT: A 99 HIS cc_start: 0.7829 (t-90) cc_final: 0.7571 (t-90) REVERT: A 154 MET cc_start: 0.9028 (mmm) cc_final: 0.8783 (mmm) REVERT: A 236 MET cc_start: 0.8199 (ttm) cc_final: 0.7117 (mtt) REVERT: A 288 MET cc_start: 0.9179 (ttt) cc_final: 0.8977 (ttt) REVERT: A 387 MET cc_start: 0.9310 (mmt) cc_final: 0.9105 (mmt) REVERT: A 528 LEU cc_start: 0.9001 (pt) cc_final: 0.8461 (tp) REVERT: B 136 LEU cc_start: 0.9245 (tt) cc_final: 0.9012 (pp) REVERT: B 379 MET cc_start: 0.8868 (mmp) cc_final: 0.8395 (mmm) REVERT: B 432 LEU cc_start: 0.9275 (mt) cc_final: 0.9001 (mt) outliers start: 3 outliers final: 0 residues processed: 142 average time/residue: 0.2113 time to fit residues: 45.1853 Evaluate side-chains 94 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 37 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN B 602 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.045298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.035142 restraints weight = 91776.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036145 restraints weight = 58022.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036879 restraints weight = 42267.191| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11636 Z= 0.262 Angle : 0.661 6.888 15696 Z= 0.349 Chirality : 0.042 0.173 1852 Planarity : 0.004 0.048 1944 Dihedral : 7.031 83.397 1620 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % 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: 0.81 (0.22), residues: 1456 helix: 1.64 (0.18), residues: 836 sheet: -0.10 (0.40), residues: 140 loop : -1.23 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 718 HIS 0.005 0.001 HIS A 660 PHE 0.026 0.002 PHE B 493 TYR 0.014 0.002 TYR B 104 ARG 0.003 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 694) hydrogen bonds : angle 4.72703 ( 2025) covalent geometry : bond 0.00537 (11636) covalent geometry : angle 0.66092 (15696) *********************** 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 111 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8791 (m-30) cc_final: 0.8549 (m-30) REVERT: A 236 MET cc_start: 0.8279 (ttm) cc_final: 0.7074 (mtt) REVERT: A 288 MET cc_start: 0.9269 (ttt) cc_final: 0.8798 (ttt) REVERT: A 387 MET cc_start: 0.9389 (mmt) cc_final: 0.9089 (mmm) REVERT: A 478 PHE cc_start: 0.8501 (m-80) cc_final: 0.8150 (m-80) REVERT: A 528 LEU cc_start: 0.9004 (pt) cc_final: 0.8272 (tp) REVERT: A 533 MET cc_start: 0.9329 (tpt) cc_final: 0.8884 (tpp) REVERT: B 25 CYS cc_start: 0.9412 (p) cc_final: 0.9079 (p) REVERT: B 379 MET cc_start: 0.8862 (mmp) cc_final: 0.8380 (mmm) REVERT: B 387 MET cc_start: 0.8970 (tmm) cc_final: 0.8757 (tmm) REVERT: B 568 ASP cc_start: 0.9501 (t70) cc_final: 0.9263 (t0) REVERT: D 19 MET cc_start: 0.8586 (mmp) cc_final: 0.8363 (mmm) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.2140 time to fit residues: 35.7712 Evaluate side-chains 88 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** B 534 ASN B 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.045717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035868 restraints weight = 90426.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.036865 restraints weight = 57965.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037586 restraints weight = 42640.528| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3221 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= 0.156 Angle : 0.553 7.601 15696 Z= 0.292 Chirality : 0.041 0.195 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.745 85.147 1620 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 1.07 (0.23), residues: 1456 helix: 1.84 (0.19), residues: 836 sheet: 0.10 (0.41), residues: 140 loop : -1.14 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 718 HIS 0.004 0.001 HIS B 207 PHE 0.013 0.001 PHE B 270 TYR 0.012 0.001 TYR B 33 ARG 0.002 0.000 ARG B 277 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 694) hydrogen bonds : angle 4.43968 ( 2025) covalent geometry : bond 0.00324 (11636) covalent geometry : angle 0.55280 (15696) *********************** 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 112 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8366 (t-90) cc_final: 0.7852 (t-90) REVERT: A 236 MET cc_start: 0.8259 (ttm) cc_final: 0.7017 (mtt) REVERT: A 288 MET cc_start: 0.9231 (ttt) cc_final: 0.8727 (ttt) REVERT: A 289 ILE cc_start: 0.9063 (mt) cc_final: 0.8855 (mt) REVERT: A 478 PHE cc_start: 0.8468 (m-80) cc_final: 0.8066 (m-80) REVERT: A 528 LEU cc_start: 0.8954 (pt) cc_final: 0.8286 (tp) REVERT: A 533 MET cc_start: 0.9205 (tpt) cc_final: 0.8842 (tpp) REVERT: B 25 CYS cc_start: 0.9361 (p) cc_final: 0.9015 (p) REVERT: B 37 MET cc_start: 0.9122 (mmm) cc_final: 0.8423 (mpp) REVERT: B 173 PHE cc_start: 0.9113 (t80) cc_final: 0.8830 (t80) REVERT: B 288 MET cc_start: 0.8370 (mmt) cc_final: 0.8125 (mmt) REVERT: B 379 MET cc_start: 0.8966 (mmp) cc_final: 0.8516 (mmm) REVERT: B 387 MET cc_start: 0.8936 (tmm) cc_final: 0.8678 (tmm) REVERT: B 432 LEU cc_start: 0.9416 (mt) cc_final: 0.9106 (mt) REVERT: B 568 ASP cc_start: 0.9519 (t70) cc_final: 0.9280 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2122 time to fit residues: 35.8325 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 : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** 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 = 0.3153 r_free = 0.3153 target = 0.045248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035606 restraints weight = 88284.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.036599 restraints weight = 56965.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037323 restraints weight = 41678.444| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3454 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= 0.144 Angle : 0.553 8.656 15696 Z= 0.292 Chirality : 0.041 0.156 1852 Planarity : 0.003 0.034 1944 Dihedral : 6.627 82.635 1620 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.08 % Allowed : 2.57 % Favored : 97.35 % 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: 1.21 (0.23), residues: 1456 helix: 2.01 (0.19), residues: 826 sheet: 0.11 (0.42), residues: 140 loop : -1.12 (0.27), residues: 490 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 0.011 0.001 PHE B 493 TYR 0.011 0.001 TYR B 33 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 694) hydrogen bonds : angle 4.30787 ( 2025) covalent geometry : bond 0.00299 (11636) covalent geometry : angle 0.55269 (15696) *********************** 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 110 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8242 (ttm) cc_final: 0.7013 (mtt) REVERT: A 288 MET cc_start: 0.9183 (ttt) cc_final: 0.8903 (ttt) REVERT: A 478 PHE cc_start: 0.8468 (m-80) cc_final: 0.8078 (m-80) REVERT: A 528 LEU cc_start: 0.8950 (pt) cc_final: 0.8297 (tp) REVERT: A 533 MET cc_start: 0.9190 (tpt) cc_final: 0.8886 (tpp) REVERT: B 88 ILE cc_start: 0.9379 (mt) cc_final: 0.9105 (mp) REVERT: B 173 PHE cc_start: 0.9141 (t80) cc_final: 0.8845 (t80) REVERT: B 288 MET cc_start: 0.8284 (mmt) cc_final: 0.8041 (mmt) REVERT: B 379 MET cc_start: 0.8946 (mmp) cc_final: 0.8428 (mmm) REVERT: B 387 MET cc_start: 0.8953 (tmm) cc_final: 0.8670 (tmm) REVERT: B 432 LEU cc_start: 0.9428 (mt) cc_final: 0.9094 (mt) REVERT: B 568 ASP cc_start: 0.9496 (t70) cc_final: 0.9264 (t0) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2273 time to fit residues: 37.1443 Evaluate side-chains 85 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 B 579 ASN B 652 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.034790 restraints weight = 93832.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035782 restraints weight = 59544.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036477 restraints weight = 43407.294| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11636 Z= 0.211 Angle : 0.605 6.775 15696 Z= 0.321 Chirality : 0.041 0.221 1852 Planarity : 0.003 0.037 1944 Dihedral : 6.677 80.542 1620 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: 1.15 (0.23), residues: 1456 helix: 1.94 (0.19), residues: 830 sheet: 0.01 (0.41), residues: 140 loop : -1.09 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 718 HIS 0.004 0.001 HIS A 660 PHE 0.016 0.002 PHE B 493 TYR 0.012 0.001 TYR B 714 ARG 0.008 0.001 ARG A 14 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 694) hydrogen bonds : angle 4.54097 ( 2025) covalent geometry : bond 0.00435 (11636) covalent geometry : angle 0.60531 (15696) *********************** 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 105 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8414 (ppp) cc_final: 0.7759 (ppp) REVERT: A 97 LEU cc_start: 0.8216 (tp) cc_final: 0.7811 (tp) REVERT: A 99 HIS cc_start: 0.8371 (t-90) cc_final: 0.7930 (t-90) REVERT: A 236 MET cc_start: 0.8256 (ttm) cc_final: 0.6968 (mtt) REVERT: A 288 MET cc_start: 0.9202 (ttt) cc_final: 0.8646 (ttt) REVERT: A 289 ILE cc_start: 0.9032 (mt) cc_final: 0.8798 (mt) REVERT: A 478 PHE cc_start: 0.8501 (m-80) cc_final: 0.8055 (m-80) REVERT: A 528 LEU cc_start: 0.9027 (pt) cc_final: 0.8317 (tp) REVERT: A 533 MET cc_start: 0.9187 (tpt) cc_final: 0.8892 (tpp) REVERT: C 19 MET cc_start: 0.9477 (mmp) cc_final: 0.9256 (mmm) REVERT: B 37 MET cc_start: 0.9250 (mmm) cc_final: 0.8824 (tpp) REVERT: B 88 ILE cc_start: 0.9417 (mt) cc_final: 0.9149 (mp) REVERT: B 379 MET cc_start: 0.8973 (mmp) cc_final: 0.8441 (mmm) REVERT: B 387 MET cc_start: 0.8839 (tmm) cc_final: 0.8604 (tmm) REVERT: B 568 ASP cc_start: 0.9484 (t70) cc_final: 0.9265 (t0) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2051 time to fit residues: 32.9919 Evaluate side-chains 85 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.044946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035322 restraints weight = 90599.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036307 restraints weight = 57690.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.037039 restraints weight = 42216.963| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3872 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= 0.132 Angle : 0.559 8.886 15696 Z= 0.292 Chirality : 0.041 0.171 1852 Planarity : 0.003 0.039 1944 Dihedral : 6.540 81.170 1620 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: 1.33 (0.23), residues: 1456 helix: 2.14 (0.19), residues: 826 sheet: 0.06 (0.41), residues: 140 loop : -1.11 (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 0.010 0.001 PHE A 213 TYR 0.011 0.001 TYR B 33 ARG 0.013 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 694) hydrogen bonds : angle 4.26201 ( 2025) covalent geometry : bond 0.00273 (11636) covalent geometry : angle 0.55939 (15696) *********************** 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 111 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8454 (t-90) cc_final: 0.7977 (t-90) REVERT: A 236 MET cc_start: 0.8186 (ttm) cc_final: 0.6990 (mtt) REVERT: A 288 MET cc_start: 0.9108 (ttt) cc_final: 0.8561 (ttt) REVERT: A 289 ILE cc_start: 0.9010 (mt) cc_final: 0.8775 (mt) REVERT: A 478 PHE cc_start: 0.8553 (m-80) cc_final: 0.8096 (m-80) REVERT: A 528 LEU cc_start: 0.8982 (pt) cc_final: 0.8306 (tp) REVERT: A 533 MET cc_start: 0.9205 (tpt) cc_final: 0.8905 (tpp) REVERT: A 717 MET cc_start: 0.9316 (ptp) cc_final: 0.9108 (ptp) REVERT: C 19 MET cc_start: 0.9469 (mmp) cc_final: 0.9249 (mmm) REVERT: B 88 ILE cc_start: 0.9405 (mt) cc_final: 0.9135 (mp) REVERT: B 173 PHE cc_start: 0.9145 (t80) cc_final: 0.8811 (t80) REVERT: B 288 MET cc_start: 0.8365 (mmt) cc_final: 0.8127 (mmt) REVERT: B 379 MET cc_start: 0.8991 (mmp) cc_final: 0.8474 (mmm) REVERT: B 387 MET cc_start: 0.8841 (tmm) cc_final: 0.8577 (tmm) REVERT: B 432 LEU cc_start: 0.9458 (mt) cc_final: 0.9124 (mt) REVERT: B 568 ASP cc_start: 0.9494 (t70) cc_final: 0.9280 (t0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2187 time to fit residues: 36.5053 Evaluate side-chains 88 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3159 r_free = 0.3159 target = 0.045259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035626 restraints weight = 89380.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.036631 restraints weight = 56957.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.037368 restraints weight = 41544.682| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4016 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= 0.120 Angle : 0.551 8.205 15696 Z= 0.285 Chirality : 0.041 0.152 1852 Planarity : 0.003 0.035 1944 Dihedral : 6.409 78.306 1620 Min Nonbonded Distance : 1.933 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: 2.23 (0.19), residues: 826 sheet: 0.10 (0.42), residues: 140 loop : -1.08 (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 213 TYR 0.010 0.001 TYR B 33 ARG 0.004 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 694) hydrogen bonds : angle 4.18080 ( 2025) covalent geometry : bond 0.00247 (11636) covalent geometry : angle 0.55110 (15696) *********************** 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 116 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8221 (ppp) cc_final: 0.7359 (ppp) REVERT: A 99 HIS cc_start: 0.8325 (t-90) cc_final: 0.7823 (t-90) REVERT: A 236 MET cc_start: 0.8187 (ttm) cc_final: 0.7022 (mtt) REVERT: A 288 MET cc_start: 0.9086 (ttt) cc_final: 0.8527 (ttt) REVERT: A 289 ILE cc_start: 0.8997 (mt) cc_final: 0.8752 (mt) REVERT: A 387 MET cc_start: 0.9429 (mmt) cc_final: 0.9170 (mmt) REVERT: A 478 PHE cc_start: 0.8516 (m-80) cc_final: 0.8086 (m-80) REVERT: A 528 LEU cc_start: 0.8950 (pt) cc_final: 0.8273 (tp) REVERT: A 533 MET cc_start: 0.9178 (tpt) cc_final: 0.8908 (tpp) REVERT: B 16 TYR cc_start: 0.7990 (m-80) cc_final: 0.7271 (m-80) REVERT: B 88 ILE cc_start: 0.9384 (mt) cc_final: 0.9126 (mp) REVERT: B 173 PHE cc_start: 0.9108 (t80) cc_final: 0.8829 (t80) REVERT: B 288 MET cc_start: 0.8349 (mmt) cc_final: 0.8126 (mmt) REVERT: B 379 MET cc_start: 0.8986 (mmp) cc_final: 0.8470 (mmm) REVERT: B 387 MET cc_start: 0.8849 (tmm) cc_final: 0.8579 (tmm) REVERT: B 432 LEU cc_start: 0.9467 (mt) cc_final: 0.9129 (mt) REVERT: B 568 ASP cc_start: 0.9516 (t70) cc_final: 0.9306 (t0) REVERT: B 612 TYR cc_start: 0.8254 (t80) cc_final: 0.8044 (t80) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2163 time to fit residues: 37.9322 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 : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 66 optimal weight: 0.0370 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.046095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036401 restraints weight = 88835.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.037421 restraints weight = 56909.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038160 restraints weight = 41652.150| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4093 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= 0.111 Angle : 0.569 8.162 15696 Z= 0.289 Chirality : 0.042 0.317 1852 Planarity : 0.003 0.051 1944 Dihedral : 6.332 77.620 1620 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 1.49 (0.23), residues: 1456 helix: 2.27 (0.19), residues: 826 sheet: 0.26 (0.43), residues: 140 loop : -1.08 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 132 HIS 0.004 0.001 HIS B 207 PHE 0.009 0.001 PHE B 604 TYR 0.009 0.001 TYR A 225 ARG 0.007 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 694) hydrogen bonds : angle 4.07680 ( 2025) covalent geometry : bond 0.00221 (11636) covalent geometry : angle 0.56941 (15696) *********************** 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 116 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8166 (ppp) cc_final: 0.7312 (ppp) REVERT: A 99 HIS cc_start: 0.8181 (t-90) cc_final: 0.7691 (t-90) REVERT: A 154 MET cc_start: 0.8919 (mmm) cc_final: 0.8606 (mmm) REVERT: A 236 MET cc_start: 0.8125 (ttm) cc_final: 0.7053 (mtt) REVERT: A 288 MET cc_start: 0.9021 (ttt) cc_final: 0.8640 (ttt) REVERT: A 387 MET cc_start: 0.9423 (mmt) cc_final: 0.9077 (mmm) REVERT: A 478 PHE cc_start: 0.8498 (m-80) cc_final: 0.8046 (m-80) REVERT: A 528 LEU cc_start: 0.8946 (pt) cc_final: 0.8311 (tp) REVERT: A 533 MET cc_start: 0.9146 (tpt) cc_final: 0.8942 (tpp) REVERT: C 19 MET cc_start: 0.9369 (mmp) cc_final: 0.9089 (mmp) REVERT: B 88 ILE cc_start: 0.9369 (mt) cc_final: 0.9116 (mp) REVERT: B 173 PHE cc_start: 0.9147 (t80) cc_final: 0.8855 (t80) REVERT: B 288 MET cc_start: 0.8328 (mmt) cc_final: 0.8101 (mmt) REVERT: B 379 MET cc_start: 0.8968 (mmp) cc_final: 0.8442 (mmm) REVERT: B 387 MET cc_start: 0.8867 (tmm) cc_final: 0.8610 (tmm) REVERT: B 432 LEU cc_start: 0.9469 (mt) cc_final: 0.9136 (mt) REVERT: B 568 ASP cc_start: 0.9516 (t70) cc_final: 0.9306 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2150 time to fit residues: 37.3646 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 : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 579 ASN ** B 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 ASN ** B 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.045554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.035894 restraints weight = 89454.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036884 restraints weight = 57802.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.037597 restraints weight = 42515.914| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4208 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= 0.126 Angle : 0.560 7.866 15696 Z= 0.288 Chirality : 0.042 0.322 1852 Planarity : 0.003 0.037 1944 Dihedral : 6.338 76.529 1620 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 1.49 (0.23), residues: 1456 helix: 2.26 (0.19), residues: 826 sheet: 0.14 (0.43), residues: 138 loop : -1.01 (0.27), residues: 492 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 326 TYR 0.009 0.001 TYR B 714 ARG 0.007 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 694) hydrogen bonds : angle 4.13518 ( 2025) covalent geometry : bond 0.00264 (11636) covalent geometry : angle 0.56016 (15696) ********************** 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 102 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8187 (ppp) cc_final: 0.7309 (ppp) REVERT: A 154 MET cc_start: 0.8949 (mmm) cc_final: 0.8635 (mmm) REVERT: A 236 MET cc_start: 0.8144 (ttm) cc_final: 0.7048 (mtt) REVERT: A 288 MET cc_start: 0.8972 (ttt) cc_final: 0.8580 (ttt) REVERT: A 387 MET cc_start: 0.9406 (mmt) cc_final: 0.9053 (mmm) REVERT: A 478 PHE cc_start: 0.8507 (m-80) cc_final: 0.8042 (m-80) REVERT: A 528 LEU cc_start: 0.9031 (pt) cc_final: 0.8404 (tp) REVERT: A 533 MET cc_start: 0.9150 (tpt) cc_final: 0.8885 (tpp) REVERT: C 19 MET cc_start: 0.9354 (mmp) cc_final: 0.9102 (mmp) REVERT: B 88 ILE cc_start: 0.9356 (mt) cc_final: 0.9110 (mp) REVERT: B 173 PHE cc_start: 0.9148 (t80) cc_final: 0.8800 (t80) REVERT: B 288 MET cc_start: 0.8318 (mmt) cc_final: 0.7993 (mmt) REVERT: B 379 MET cc_start: 0.8960 (mmp) cc_final: 0.8413 (mmm) REVERT: B 387 MET cc_start: 0.8872 (tmm) cc_final: 0.8609 (tmm) REVERT: B 432 LEU cc_start: 0.9447 (mt) cc_final: 0.9081 (mt) REVERT: B 612 TYR cc_start: 0.8440 (t80) cc_final: 0.8156 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2006 time to fit residues: 32.1066 Evaluate side-chains 85 residues out of total 1252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.045161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035500 restraints weight = 94720.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036512 restraints weight = 59917.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037232 restraints weight = 43740.924| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11636 Z= 0.174 Angle : 0.596 7.461 15696 Z= 0.310 Chirality : 0.042 0.304 1852 Planarity : 0.003 0.040 1944 Dihedral : 6.438 77.237 1620 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 1.53 (0.23), residues: 1456 helix: 2.26 (0.19), residues: 824 sheet: 0.05 (0.43), residues: 138 loop : -0.89 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 718 HIS 0.004 0.001 HIS A 660 PHE 0.019 0.002 PHE B 326 TYR 0.017 0.001 TYR B 714 ARG 0.005 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 694) hydrogen bonds : angle 4.33195 ( 2025) covalent geometry : bond 0.00364 (11636) covalent geometry : angle 0.59602 (15696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.01 seconds wall clock time: 66 minutes 0.12 seconds (3960.12 seconds total)