Starting phenix.real_space_refine on Sun Aug 24 03:16:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cmt_16745/08_2025/8cmt_16745_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cmt_16745/08_2025/8cmt_16745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cmt_16745/08_2025/8cmt_16745_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cmt_16745/08_2025/8cmt_16745_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cmt_16745/08_2025/8cmt_16745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cmt_16745/08_2025/8cmt_16745.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 10462 2.51 5 N 2818 2.21 5 O 3140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 117 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5791 Classifications: {'peptide': 722} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 685} Chain: "B" Number of atoms: 5791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5791 Classifications: {'peptide': 722} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 32, 'TRANS': 686} Chain: "C" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2468 Classifications: {'peptide': 307} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 288} Chain: "D" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2468 Classifications: {'peptide': 307} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 288} Time building chain proxies: 3.97, per 1000 atoms: 0.24 Number of scatterers: 16518 At special positions: 0 Unit cell: (121.278, 130.339, 138.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 3140 8.00 N 2818 7.00 C 10462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 255 " distance=2.02 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 316 " distance=2.02 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 327 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 59 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 135 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 197 " distance=2.04 Simple disulfide: pdb=" SG CYS D 180 " - pdb=" SG CYS D 208 " distance=2.03 Simple disulfide: pdb=" SG CYS D 213 " - pdb=" SG CYS D 255 " distance=2.04 Simple disulfide: pdb=" SG CYS D 241 " - pdb=" SG CYS D 267 " distance=2.05 Simple disulfide: pdb=" SG CYS D 274 " - pdb=" SG CYS D 316 " distance=2.02 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 327 " distance=2.04 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: 1.49 Conformation dependent library (CDL) restraints added in 604.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3816 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 46 sheets defined 14.7% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 234 through 246 Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.757A pdb=" N ALA A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 3.777A pdb=" N TRP A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 307 removed outlier: 4.595A pdb=" N ILE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.854A pdb=" N HIS A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 removed outlier: 3.732A pdb=" N VAL A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.689A pdb=" N TYR A 482 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 501 removed outlier: 3.729A pdb=" N ARG A 492 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 4.440A pdb=" N GLY A 511 " --> pdb=" O ASN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.962A pdb=" N TYR A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 234 through 246 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.760A pdb=" N ALA B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 293 removed outlier: 3.866A pdb=" N TRP B 293 " --> pdb=" O PRO B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.686A pdb=" N HIS B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 438 removed outlier: 3.866A pdb=" N VAL B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.660A pdb=" N TYR B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 501 removed outlier: 3.567A pdb=" N ARG B 492 " --> pdb=" O GLN B 488 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 501 " --> pdb=" O THR B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.837A pdb=" N TYR B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'C' and resid 37 through 42 removed outlier: 4.268A pdb=" N THR C 41 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'D' and resid 37 through 42 removed outlier: 4.172A pdb=" N THR D 41 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.885A pdb=" N VAL A 102 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 6.843A pdb=" N ASP A 88 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 51 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN A 86 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG A 138 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG A 144 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 217 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 278 removed outlier: 4.579A pdb=" N TYR A 312 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 414 removed outlier: 6.286A pdb=" N TYR A 408 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N THR A 399 " --> pdb=" O TYR A 408 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA A 395 " --> pdb=" O PRO A 412 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER A 414 " --> pdb=" O TRP A 393 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N TRP A 393 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER A 398 " --> pdb=" O CYS A 375 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N CYS A 375 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 14.800A pdb=" N TYR A 373 " --> pdb=" O PRO A 400 " (cutoff:3.500A) removed outlier: 16.292A pdb=" N GLU A 402 " --> pdb=" O TRP A 371 " (cutoff:3.500A) removed outlier: 15.013A pdb=" N TRP A 371 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN A 372 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE A 335 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS A 468 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 355 removed outlier: 6.197A pdb=" N THR A 444 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 453 " --> pdb=" O THR A 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 519 through 525 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 578 removed outlier: 6.875A pdb=" N ILE A 558 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A 568 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA A 556 " --> pdb=" O GLU A 568 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 570 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 554 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU A 572 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA A 552 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 574 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 550 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 576 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR A 548 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 604 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 634 through 638 Processing sheet with id=AB2, first strand: chain 'A' and resid 674 through 684 removed outlier: 5.236A pdb=" N ARG A 675 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLY A 670 " --> pdb=" O ARG A 675 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 683 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG A 662 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 718 " --> pdb=" O MET A 710 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 30 through 32 Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 32 removed outlier: 4.609A pdb=" N LEU B 99 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 102 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 48 through 52 removed outlier: 6.782A pdb=" N ASP B 88 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 51 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN B 86 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG B 138 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG B 144 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 135 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 210 through 217 removed outlier: 3.570A pdb=" N GLU B 217 " --> pdb=" O ASP B 220 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 276 through 278 removed outlier: 4.556A pdb=" N TYR B 312 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 407 through 414 removed outlier: 4.258A pdb=" N MET B 407 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN B 401 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG B 409 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR B 399 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLY B 411 " --> pdb=" O ASP B 397 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASP B 397 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER B 398 " --> pdb=" O CYS B 375 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N CYS B 375 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 14.558A pdb=" N TYR B 373 " --> pdb=" O PRO B 400 " (cutoff:3.500A) removed outlier: 16.011A pdb=" N GLU B 402 " --> pdb=" O TRP B 371 " (cutoff:3.500A) removed outlier: 14.901A pdb=" N TRP B 371 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 372 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE B 335 " --> pdb=" O LYS B 468 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS B 468 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU B 464 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 350 through 355 removed outlier: 6.371A pdb=" N THR B 444 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL B 453 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 519 through 525 Processing sheet with id=AC2, first strand: chain 'B' and resid 565 through 578 removed outlier: 5.891A pdb=" N GLU B 568 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 558 " --> pdb=" O GLU B 568 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 570 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 604 " --> pdb=" O THR B 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 634 through 638 Processing sheet with id=AC4, first strand: chain 'B' and resid 674 through 684 removed outlier: 5.204A pdb=" N ARG B 675 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY B 670 " --> pdb=" O ARG B 675 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU B 683 " --> pdb=" O ARG B 662 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG B 662 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL B 718 " --> pdb=" O MET B 710 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC6, first strand: chain 'C' and resid 63 through 64 Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'C' and resid 99 through 101 Processing sheet with id=AC9, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AD1, first strand: chain 'C' and resid 152 through 154 Processing sheet with id=AD2, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AD3, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AD4, first strand: chain 'C' and resid 222 through 224 Processing sheet with id=AD5, first strand: chain 'C' and resid 246 through 248 Processing sheet with id=AD6, first strand: chain 'C' and resid 283 through 285 Processing sheet with id=AD7, first strand: chain 'C' and resid 306 through 309 Processing sheet with id=AD8, first strand: chain 'D' and resid 33 through 35 Processing sheet with id=AD9, first strand: chain 'D' and resid 63 through 65 Processing sheet with id=AE1, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AE2, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AE3, first strand: chain 'D' and resid 122 through 124 Processing sheet with id=AE4, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AE5, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AE7, first strand: chain 'D' and resid 222 through 224 removed outlier: 4.510A pdb=" N VAL D 236 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 253 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 246 through 248 Processing sheet with id=AE9, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AF1, first strand: chain 'D' and resid 306 through 309 558 hydrogen bonds defined for protein. 1500 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: 3.99 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3181 1.32 - 1.44: 4254 1.44 - 1.57: 9361 1.57 - 1.69: 0 1.69 - 1.82: 138 Bond restraints: 16934 Sorted by residual: bond pdb=" CA PRO C 275 " pdb=" C PRO C 275 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.49e+01 bond pdb=" C ARG B 409 " pdb=" O ARG B 409 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.24e-02 6.50e+03 1.31e+01 bond pdb=" CA PRO C 324 " pdb=" C PRO C 324 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.20e+01 bond pdb=" CZ ARG A 159 " pdb=" NH2 ARG A 159 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.15e+01 bond pdb=" C GLY B 406 " pdb=" O GLY B 406 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.35e-02 5.49e+03 1.14e+01 ... (remaining 16929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 17397 2.01 - 4.02: 5088 4.02 - 6.02: 433 6.02 - 8.03: 39 8.03 - 10.04: 7 Bond angle restraints: 22964 Sorted by residual: angle pdb=" CA PRO C 24 " pdb=" N PRO C 24 " pdb=" CD PRO C 24 " ideal model delta sigma weight residual 112.00 103.09 8.91 1.40e+00 5.10e-01 4.05e+01 angle pdb=" CA ASN A 372 " pdb=" CB ASN A 372 " pdb=" CG ASN A 372 " ideal model delta sigma weight residual 112.60 118.62 -6.02 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CA PRO D 226 " pdb=" N PRO D 226 " pdb=" CD PRO D 226 " ideal model delta sigma weight residual 112.00 103.72 8.28 1.40e+00 5.10e-01 3.50e+01 angle pdb=" CA ARG B 311 " pdb=" C ARG B 311 " pdb=" N TYR B 312 " ideal model delta sigma weight residual 116.37 123.16 -6.79 1.19e+00 7.06e-01 3.25e+01 angle pdb=" CA ASP B 618 " pdb=" CB ASP B 618 " pdb=" CG ASP B 618 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.00e+00 1.00e+00 3.17e+01 ... (remaining 22959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 9365 17.83 - 35.66: 582 35.66 - 53.49: 111 53.49 - 71.32: 49 71.32 - 89.14: 24 Dihedral angle restraints: 10131 sinusoidal: 4159 harmonic: 5972 Sorted by residual: dihedral pdb=" CD ARG D 270 " pdb=" NE ARG D 270 " pdb=" CZ ARG D 270 " pdb=" NH1 ARG D 270 " ideal model delta sinusoidal sigma weight residual 0.00 87.09 -87.09 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CD ARG C 147 " pdb=" NE ARG C 147 " pdb=" CZ ARG C 147 " pdb=" NH1 ARG C 147 " ideal model delta sinusoidal sigma weight residual 0.00 86.94 -86.94 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CD ARG D 271 " pdb=" NE ARG D 271 " pdb=" CZ ARG D 271 " pdb=" NH1 ARG D 271 " ideal model delta sinusoidal sigma weight residual 0.00 -80.72 80.72 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 10128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1876 0.111 - 0.222: 512 0.222 - 0.333: 46 0.333 - 0.443: 8 0.443 - 0.554: 2 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CA ASN D 244 " pdb=" N ASN D 244 " pdb=" C ASN D 244 " pdb=" CB ASN D 244 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CA PRO D 226 " pdb=" N PRO D 226 " pdb=" C PRO D 226 " pdb=" CB PRO D 226 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA LYS C 173 " pdb=" N LYS C 173 " pdb=" C LYS C 173 " pdb=" CB LYS C 173 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2441 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG C 147 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 270 " -1.093 9.50e-02 1.11e+02 4.90e-01 1.45e+02 pdb=" NE ARG D 270 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 270 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 270 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG D 270 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 271 " -1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG D 271 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG D 271 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 271 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG D 271 " -0.019 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 13 2.54 - 3.13: 11738 3.13 - 3.72: 24860 3.72 - 4.31: 37304 4.31 - 4.90: 61423 Nonbonded interactions: 135338 Sorted by model distance: nonbonded pdb=" OE2 GLU A 652 " pdb=" NE2 GLN A 691 " model vdw 1.953 3.120 nonbonded pdb=" O GLY D 121 " pdb=" N GLU D 149 " model vdw 2.217 3.120 nonbonded pdb=" O SER A 544 " pdb=" N LEU A 581 " model vdw 2.296 3.120 nonbonded pdb=" O ASP B 94 " pdb=" N ARG B 97 " model vdw 2.344 3.120 nonbonded pdb=" OH TYR A 284 " pdb=" OE2 GLU A 601 " model vdw 2.360 3.040 ... (remaining 135333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 12.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.820 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 : 0.012 0.049 16951 Z= 0.748 Angle : 1.743 10.037 22998 Z= 1.169 Chirality : 0.095 0.554 2444 Planarity : 0.027 0.493 2988 Dihedral : 13.754 89.144 6264 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.51 % Favored : 96.34 % Rotamer: Outliers : 1.81 % Allowed : 3.79 % Favored : 94.40 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2050 helix: -1.26 (0.30), residues: 196 sheet: 0.92 (0.20), residues: 566 loop : -0.42 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 516 TYR 0.138 0.018 TYR B 284 PHE 0.066 0.014 PHE A 608 TRP 0.114 0.021 TRP A 316 HIS 0.010 0.003 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.01240 (16934) covalent geometry : angle 1.74395 (22964) SS BOND : bond 0.00737 ( 17) SS BOND : angle 1.18961 ( 34) hydrogen bonds : bond 0.13398 ( 546) hydrogen bonds : angle 8.12509 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7082 (pp20) REVERT: A 220 ASP cc_start: 0.8141 (t0) cc_final: 0.7806 (p0) REVERT: A 346 ASP cc_start: 0.8795 (t0) cc_final: 0.8587 (t70) REVERT: A 571 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8468 (ptmt) REVERT: A 617 ARG cc_start: 0.7951 (mmp-170) cc_final: 0.7730 (mmp-170) REVERT: A 658 LYS cc_start: 0.7684 (mmpt) cc_final: 0.6824 (mtmm) REVERT: A 675 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8167 (mtp-110) REVERT: B 130 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7808 (mptt) REVERT: B 167 PRO cc_start: 0.9144 (Cg_exo) cc_final: 0.8932 (Cg_endo) REVERT: B 220 ASP cc_start: 0.8287 (t0) cc_final: 0.7776 (t70) REVERT: B 248 MET cc_start: 0.8314 (ttt) cc_final: 0.8102 (ttm) REVERT: B 476 MET cc_start: 0.8333 (ttm) cc_final: 0.8018 (ttt) REVERT: B 491 GLU cc_start: 0.8164 (tt0) cc_final: 0.7828 (tt0) REVERT: B 520 ASP cc_start: 0.7918 (m-30) cc_final: 0.7522 (p0) REVERT: B 541 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7185 (ttp-170) REVERT: B 584 LYS cc_start: 0.8556 (tttt) cc_final: 0.8287 (tptp) REVERT: B 596 MET cc_start: 0.8399 (mmm) cc_final: 0.8139 (mmm) REVERT: B 645 SER cc_start: 0.9133 (m) cc_final: 0.8805 (p) REVERT: B 677 MET cc_start: 0.7389 (mtt) cc_final: 0.7100 (mtt) REVERT: B 687 ASN cc_start: 0.8228 (m-40) cc_final: 0.7986 (p0) REVERT: C 34 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7376 (mmm160) REVERT: C 108 TYR cc_start: 0.7370 (m-80) cc_final: 0.7133 (m-80) REVERT: C 125 THR cc_start: 0.7457 (m) cc_final: 0.7175 (m) REVERT: D 34 ARG cc_start: 0.8645 (mmt-90) cc_final: 0.8371 (mmt-90) REVERT: D 93 LYS cc_start: 0.7951 (tttt) cc_final: 0.7680 (ttmt) outliers start: 33 outliers final: 5 residues processed: 347 average time/residue: 0.1872 time to fit residues: 87.1535 Evaluate side-chains 176 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain C residue 24 PRO Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 271 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 606 HIS A 614 ASN A 623 GLN B 198 ASN B 543 ASN B 725 GLN C 37 GLN C 73 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.129275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083065 restraints weight = 28605.292| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.58 r_work: 0.2971 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16951 Z= 0.142 Angle : 0.586 13.282 22998 Z= 0.316 Chirality : 0.046 0.255 2444 Planarity : 0.006 0.165 2988 Dihedral : 5.853 59.865 2282 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.29 % Rotamer: Outliers : 1.59 % Allowed : 7.68 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2050 helix: 0.16 (0.33), residues: 196 sheet: 0.87 (0.20), residues: 639 loop : 0.15 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 612 TYR 0.014 0.001 TYR C 261 PHE 0.023 0.002 PHE D 224 TRP 0.017 0.002 TRP A 280 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00319 (16934) covalent geometry : angle 0.58454 (22964) SS BOND : bond 0.00281 ( 17) SS BOND : angle 1.13697 ( 34) hydrogen bonds : bond 0.03573 ( 546) hydrogen bonds : angle 5.88982 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8323 (mmt90) cc_final: 0.7519 (mmt90) REVERT: A 220 ASP cc_start: 0.8274 (t0) cc_final: 0.7632 (p0) REVERT: A 249 ASP cc_start: 0.8527 (t0) cc_final: 0.8308 (t0) REVERT: A 286 TYR cc_start: 0.8448 (m-80) cc_final: 0.8201 (m-80) REVERT: A 521 MET cc_start: 0.8624 (ttp) cc_final: 0.8229 (ttp) REVERT: A 571 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8731 (ptpt) REVERT: A 612 ARG cc_start: 0.7950 (ptm160) cc_final: 0.7182 (ptm160) REVERT: A 658 LYS cc_start: 0.7840 (mmpt) cc_final: 0.6941 (mtmm) REVERT: A 675 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.8388 (mtp-110) REVERT: B 43 GLN cc_start: 0.7719 (mp10) cc_final: 0.7494 (mp10) REVERT: B 130 LYS cc_start: 0.8462 (mmmm) cc_final: 0.8072 (mptt) REVERT: B 476 MET cc_start: 0.8664 (ttm) cc_final: 0.8269 (ttt) REVERT: B 520 ASP cc_start: 0.8568 (m-30) cc_final: 0.7826 (p0) REVERT: B 541 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7186 (ttm110) REVERT: B 584 LYS cc_start: 0.8587 (tttt) cc_final: 0.8097 (tptt) REVERT: B 596 MET cc_start: 0.8552 (mmm) cc_final: 0.8209 (mmm) REVERT: B 645 SER cc_start: 0.9105 (m) cc_final: 0.8687 (p) REVERT: B 677 MET cc_start: 0.7670 (mtt) cc_final: 0.7341 (mtt) REVERT: B 687 ASN cc_start: 0.8388 (m-40) cc_final: 0.7891 (p0) REVERT: B 697 ARG cc_start: 0.8955 (ttm-80) cc_final: 0.8704 (mtp85) REVERT: C 143 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7781 (tp40) REVERT: D 29 HIS cc_start: 0.8014 (t-90) cc_final: 0.7713 (t-90) REVERT: D 93 LYS cc_start: 0.8054 (tttt) cc_final: 0.7764 (ttmt) REVERT: D 272 ASN cc_start: 0.5924 (m-40) cc_final: 0.5675 (m-40) outliers start: 29 outliers final: 12 residues processed: 211 average time/residue: 0.1766 time to fit residues: 51.9062 Evaluate side-chains 170 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 157 optimal weight: 0.0040 chunk 33 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.6952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 372 ASN A 422 HIS A 623 GLN B 703 HIS C 37 GLN C 254 GLN D 32 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081024 restraints weight = 29355.822| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.63 r_work: 0.2908 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16951 Z= 0.113 Angle : 0.519 14.579 22998 Z= 0.277 Chirality : 0.044 0.247 2444 Planarity : 0.005 0.167 2988 Dihedral : 4.989 58.557 2271 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Rotamer: Outliers : 1.21 % Allowed : 8.29 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2050 helix: 0.44 (0.34), residues: 198 sheet: 0.96 (0.20), residues: 643 loop : 0.20 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 617 TYR 0.014 0.001 TYR C 108 PHE 0.024 0.002 PHE D 224 TRP 0.013 0.001 TRP A 280 HIS 0.003 0.001 HIS A 545 Details of bonding type rmsd covalent geometry : bond 0.00255 (16934) covalent geometry : angle 0.51704 (22964) SS BOND : bond 0.00233 ( 17) SS BOND : angle 1.16965 ( 34) hydrogen bonds : bond 0.03115 ( 546) hydrogen bonds : angle 5.38136 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: A 123 VAL cc_start: 0.9271 (m) cc_final: 0.9054 (p) REVERT: A 286 TYR cc_start: 0.8496 (m-80) cc_final: 0.8260 (m-80) REVERT: A 364 LYS cc_start: 0.8737 (mppt) cc_final: 0.8408 (mptt) REVERT: A 521 MET cc_start: 0.8651 (ttp) cc_final: 0.8349 (ttp) REVERT: A 571 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8761 (ptpt) REVERT: A 612 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6325 (ttm-80) REVERT: A 658 LYS cc_start: 0.7892 (mmpt) cc_final: 0.6974 (mtmm) REVERT: A 675 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8420 (mtp-110) REVERT: A 677 MET cc_start: 0.7168 (mtt) cc_final: 0.6838 (mtt) REVERT: B 130 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8210 (mptt) REVERT: B 476 MET cc_start: 0.8693 (ttm) cc_final: 0.8307 (ttt) REVERT: B 513 MET cc_start: 0.8202 (mmt) cc_final: 0.7980 (mmt) REVERT: B 520 ASP cc_start: 0.8637 (m-30) cc_final: 0.7844 (p0) REVERT: B 541 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7256 (ttm-80) REVERT: B 584 LYS cc_start: 0.8568 (tttt) cc_final: 0.8053 (tptt) REVERT: B 596 MET cc_start: 0.8526 (mmm) cc_final: 0.8202 (mmm) REVERT: B 618 ASP cc_start: 0.8138 (m-30) cc_final: 0.7850 (m-30) REVERT: B 645 SER cc_start: 0.9082 (m) cc_final: 0.8644 (p) REVERT: B 687 ASN cc_start: 0.8496 (m-40) cc_final: 0.8031 (p0) REVERT: B 697 ARG cc_start: 0.8943 (ttm-80) cc_final: 0.8721 (mtp85) REVERT: C 143 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7736 (tp-100) REVERT: D 29 HIS cc_start: 0.8015 (t-90) cc_final: 0.7704 (t-90) REVERT: D 93 LYS cc_start: 0.7967 (tttt) cc_final: 0.7723 (ttmt) REVERT: D 272 ASN cc_start: 0.6087 (m-40) cc_final: 0.5774 (m-40) outliers start: 22 outliers final: 12 residues processed: 176 average time/residue: 0.1761 time to fit residues: 43.2846 Evaluate side-chains 161 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 197 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 606 HIS B 703 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.126317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080288 restraints weight = 29098.725| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.62 r_work: 0.2885 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16951 Z= 0.130 Angle : 0.503 14.497 22998 Z= 0.267 Chirality : 0.044 0.249 2444 Planarity : 0.005 0.166 2988 Dihedral : 4.717 55.629 2271 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.85 % Rotamer: Outliers : 1.10 % Allowed : 9.00 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2050 helix: 0.56 (0.35), residues: 204 sheet: 0.91 (0.20), residues: 645 loop : 0.20 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 612 TYR 0.014 0.001 TYR C 108 PHE 0.021 0.002 PHE D 224 TRP 0.012 0.001 TRP A 280 HIS 0.005 0.001 HIS D 150 Details of bonding type rmsd covalent geometry : bond 0.00300 (16934) covalent geometry : angle 0.50166 (22964) SS BOND : bond 0.00189 ( 17) SS BOND : angle 1.11665 ( 34) hydrogen bonds : bond 0.03002 ( 546) hydrogen bonds : angle 5.16027 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 VAL cc_start: 0.9284 (m) cc_final: 0.9047 (p) REVERT: A 141 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7771 (mmt90) REVERT: A 286 TYR cc_start: 0.8526 (m-80) cc_final: 0.8289 (m-80) REVERT: A 521 MET cc_start: 0.8750 (ttp) cc_final: 0.8517 (ttp) REVERT: A 571 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8795 (ptpt) REVERT: A 658 LYS cc_start: 0.7994 (mmpt) cc_final: 0.7025 (mtmm) REVERT: A 669 ASP cc_start: 0.8711 (t70) cc_final: 0.8472 (t0) REVERT: A 675 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8360 (mtp-110) REVERT: A 677 MET cc_start: 0.7192 (mtt) cc_final: 0.6927 (mtt) REVERT: B 130 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8314 (mptt) REVERT: B 408 TYR cc_start: 0.8496 (m-80) cc_final: 0.8271 (m-80) REVERT: B 508 ASN cc_start: 0.8802 (p0) cc_final: 0.8264 (t0) REVERT: B 520 ASP cc_start: 0.8747 (m-30) cc_final: 0.7901 (p0) REVERT: B 541 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7239 (ttm110) REVERT: B 584 LYS cc_start: 0.8471 (tttt) cc_final: 0.7967 (tptt) REVERT: B 596 MET cc_start: 0.8520 (mmm) cc_final: 0.8175 (mmm) REVERT: B 618 ASP cc_start: 0.8224 (m-30) cc_final: 0.7901 (m-30) REVERT: B 645 SER cc_start: 0.9074 (m) cc_final: 0.8521 (p) REVERT: B 687 ASN cc_start: 0.8561 (m-40) cc_final: 0.8064 (p0) REVERT: C 171 LYS cc_start: 0.8615 (mttt) cc_final: 0.8322 (mmmt) REVERT: D 51 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8243 (mm) REVERT: D 69 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7902 (mtp180) REVERT: D 93 LYS cc_start: 0.7794 (tttt) cc_final: 0.7569 (ttmt) REVERT: D 272 ASN cc_start: 0.6146 (m-40) cc_final: 0.5814 (m-40) outliers start: 20 outliers final: 13 residues processed: 175 average time/residue: 0.1691 time to fit residues: 42.0879 Evaluate side-chains 161 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 181 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 193 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 606 HIS B 343 HIS B 703 HIS C 229 GLN C 254 GLN D 242 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.077534 restraints weight = 29113.714| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.57 r_work: 0.2838 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16951 Z= 0.232 Angle : 0.562 10.028 22998 Z= 0.299 Chirality : 0.046 0.193 2444 Planarity : 0.005 0.149 2988 Dihedral : 4.940 58.511 2271 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 1.48 % Allowed : 9.33 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2050 helix: 0.13 (0.35), residues: 208 sheet: 0.66 (0.20), residues: 651 loop : 0.05 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 612 TYR 0.017 0.002 TYR C 108 PHE 0.023 0.002 PHE D 224 TRP 0.013 0.002 TRP A 280 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00544 (16934) covalent geometry : angle 0.56000 (22964) SS BOND : bond 0.00324 ( 17) SS BOND : angle 1.20625 ( 34) hydrogen bonds : bond 0.03540 ( 546) hydrogen bonds : angle 5.30498 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8413 (mmt90) cc_final: 0.7484 (mmt90) REVERT: A 220 ASP cc_start: 0.8325 (t0) cc_final: 0.7589 (p0) REVERT: A 273 GLU cc_start: 0.8101 (tp30) cc_final: 0.7865 (mm-30) REVERT: A 521 MET cc_start: 0.8794 (ttp) cc_final: 0.8571 (ttp) REVERT: A 675 ARG cc_start: 0.8811 (mtm-85) cc_final: 0.8450 (mtp-110) REVERT: B 97 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.8005 (ttp-110) REVERT: B 130 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8539 (mptt) REVERT: B 196 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9111 (tt) REVERT: B 407 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8188 (tpt) REVERT: B 508 ASN cc_start: 0.8903 (p0) cc_final: 0.8371 (t0) REVERT: B 520 ASP cc_start: 0.8921 (m-30) cc_final: 0.8010 (p0) REVERT: B 541 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7104 (ttm110) REVERT: B 560 PHE cc_start: 0.8497 (m-80) cc_final: 0.8253 (m-80) REVERT: B 645 SER cc_start: 0.8997 (m) cc_final: 0.8435 (p) REVERT: B 687 ASN cc_start: 0.8759 (m-40) cc_final: 0.8294 (p0) REVERT: D 69 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7934 (mtp180) REVERT: D 272 ASN cc_start: 0.6149 (m-40) cc_final: 0.5793 (m-40) outliers start: 27 outliers final: 19 residues processed: 168 average time/residue: 0.1711 time to fit residues: 40.6871 Evaluate side-chains 158 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 160 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 72 optimal weight: 0.0980 chunk 189 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 360 ASN B 542 ASN B 703 HIS C 229 GLN C 254 GLN D 244 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081656 restraints weight = 28748.857| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.59 r_work: 0.2948 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16951 Z= 0.117 Angle : 0.496 18.955 22998 Z= 0.259 Chirality : 0.044 0.241 2444 Planarity : 0.005 0.177 2988 Dihedral : 4.641 54.157 2271 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 1.15 % Allowed : 10.21 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.19), residues: 2050 helix: 0.50 (0.36), residues: 204 sheet: 0.69 (0.20), residues: 651 loop : 0.10 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 728 TYR 0.014 0.001 TYR C 108 PHE 0.019 0.001 PHE D 224 TRP 0.011 0.001 TRP A 280 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00269 (16934) covalent geometry : angle 0.49495 (22964) SS BOND : bond 0.00177 ( 17) SS BOND : angle 1.03012 ( 34) hydrogen bonds : bond 0.02823 ( 546) hydrogen bonds : angle 5.01663 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8521 (mmt90) cc_final: 0.7629 (mmt90) REVERT: A 220 ASP cc_start: 0.8333 (t0) cc_final: 0.7649 (p0) REVERT: A 521 MET cc_start: 0.8747 (ttp) cc_final: 0.8530 (ttp) REVERT: A 675 ARG cc_start: 0.8805 (mtm-85) cc_final: 0.8497 (mtp-110) REVERT: A 677 MET cc_start: 0.7163 (mtt) cc_final: 0.6880 (mtt) REVERT: B 97 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.8012 (ttp-110) REVERT: B 130 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8571 (mptt) REVERT: B 408 TYR cc_start: 0.8611 (m-80) cc_final: 0.8350 (m-80) REVERT: B 508 ASN cc_start: 0.8879 (p0) cc_final: 0.8369 (t0) REVERT: B 520 ASP cc_start: 0.8896 (m-30) cc_final: 0.8128 (p0) REVERT: B 541 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7248 (ttm-80) REVERT: B 584 LYS cc_start: 0.8337 (tttt) cc_final: 0.7842 (tptt) REVERT: B 645 SER cc_start: 0.9082 (m) cc_final: 0.8572 (p) REVERT: B 687 ASN cc_start: 0.8612 (m-40) cc_final: 0.8205 (p0) REVERT: C 171 LYS cc_start: 0.8632 (mttt) cc_final: 0.8315 (mmmt) REVERT: D 69 ARG cc_start: 0.8238 (mmm-85) cc_final: 0.7974 (mtp180) REVERT: D 272 ASN cc_start: 0.6171 (m-40) cc_final: 0.5811 (m-40) outliers start: 21 outliers final: 13 residues processed: 153 average time/residue: 0.1817 time to fit residues: 38.9547 Evaluate side-chains 148 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN B 703 HIS C 254 GLN D 244 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077971 restraints weight = 28425.098| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.61 r_work: 0.2867 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16951 Z= 0.222 Angle : 0.551 21.565 22998 Z= 0.287 Chirality : 0.046 0.224 2444 Planarity : 0.005 0.183 2988 Dihedral : 4.788 56.617 2271 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.32 % Allowed : 10.32 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.18), residues: 2050 helix: 0.21 (0.35), residues: 208 sheet: 0.61 (0.20), residues: 645 loop : -0.00 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.018 0.001 TYR C 108 PHE 0.022 0.002 PHE D 224 TRP 0.013 0.001 TRP A 280 HIS 0.005 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00523 (16934) covalent geometry : angle 0.55011 (22964) SS BOND : bond 0.00256 ( 17) SS BOND : angle 1.06019 ( 34) hydrogen bonds : bond 0.03306 ( 546) hydrogen bonds : angle 5.17799 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8287 (t0) cc_final: 0.7472 (p0) REVERT: A 521 MET cc_start: 0.8788 (ttp) cc_final: 0.8560 (ttp) REVERT: A 675 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8380 (mtp-110) REVERT: B 97 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8080 (ttp-110) REVERT: B 130 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8337 (mmtt) REVERT: B 407 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8114 (tpt) REVERT: B 408 TYR cc_start: 0.8554 (m-80) cc_final: 0.8343 (m-80) REVERT: B 508 ASN cc_start: 0.8922 (p0) cc_final: 0.8336 (t0) REVERT: B 520 ASP cc_start: 0.8948 (m-30) cc_final: 0.8090 (p0) REVERT: B 541 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: B 560 PHE cc_start: 0.8543 (m-80) cc_final: 0.8153 (m-80) REVERT: B 584 LYS cc_start: 0.8143 (tttt) cc_final: 0.7872 (tptp) REVERT: B 645 SER cc_start: 0.8957 (m) cc_final: 0.8362 (p) REVERT: B 687 ASN cc_start: 0.8796 (m-40) cc_final: 0.8294 (p0) REVERT: C 171 LYS cc_start: 0.8607 (mttt) cc_final: 0.8308 (mmmt) REVERT: D 69 ARG cc_start: 0.8144 (mmm-85) cc_final: 0.7879 (mtp180) REVERT: D 272 ASN cc_start: 0.6121 (m-40) cc_final: 0.5779 (m-40) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.1812 time to fit residues: 39.1899 Evaluate side-chains 157 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 244 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 109 optimal weight: 0.6980 chunk 81 optimal weight: 0.0570 chunk 159 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN B 703 HIS C 254 GLN D 244 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.125909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.079519 restraints weight = 28571.731| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.63 r_work: 0.2895 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16951 Z= 0.140 Angle : 0.508 15.923 22998 Z= 0.266 Chirality : 0.044 0.196 2444 Planarity : 0.005 0.164 2988 Dihedral : 4.648 54.403 2271 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Rotamer: Outliers : 1.04 % Allowed : 10.92 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.19), residues: 2050 helix: 0.45 (0.36), residues: 204 sheet: 0.65 (0.20), residues: 643 loop : 0.00 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 729 TYR 0.018 0.001 TYR D 245 PHE 0.018 0.001 PHE D 224 TRP 0.011 0.001 TRP A 280 HIS 0.003 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00326 (16934) covalent geometry : angle 0.50689 (22964) SS BOND : bond 0.00255 ( 17) SS BOND : angle 1.00941 ( 34) hydrogen bonds : bond 0.02908 ( 546) hydrogen bonds : angle 5.02948 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8244 (t0) cc_final: 0.7417 (p0) REVERT: A 547 ARG cc_start: 0.8736 (ttt90) cc_final: 0.8506 (ttt90) REVERT: A 675 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8342 (mtp-110) REVERT: B 97 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8062 (ttp-110) REVERT: B 130 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8308 (mmtt) REVERT: B 408 TYR cc_start: 0.8474 (m-80) cc_final: 0.8206 (m-80) REVERT: B 520 ASP cc_start: 0.8909 (m-30) cc_final: 0.8062 (p0) REVERT: B 541 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7146 (ttm-80) REVERT: B 560 PHE cc_start: 0.8521 (m-80) cc_final: 0.8214 (m-80) REVERT: B 584 LYS cc_start: 0.8132 (tttt) cc_final: 0.7756 (tptp) REVERT: B 645 SER cc_start: 0.8961 (m) cc_final: 0.8359 (p) REVERT: B 680 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7423 (tpt) REVERT: B 687 ASN cc_start: 0.8781 (m-40) cc_final: 0.8264 (p0) REVERT: D 69 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7879 (mtp180) REVERT: D 272 ASN cc_start: 0.6106 (m-40) cc_final: 0.5756 (m-40) outliers start: 19 outliers final: 16 residues processed: 152 average time/residue: 0.1761 time to fit residues: 37.7186 Evaluate side-chains 150 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 627 VAL Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 157 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN B 703 HIS B 725 GLN C 229 GLN C 254 GLN D 113 ASN D 244 ASN D 254 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076211 restraints weight = 28879.409| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.61 r_work: 0.2827 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 16951 Z= 0.324 Angle : 0.628 24.031 22998 Z= 0.327 Chirality : 0.048 0.224 2444 Planarity : 0.006 0.190 2988 Dihedral : 5.049 59.639 2271 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 10.37 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.18), residues: 2050 helix: -0.03 (0.35), residues: 212 sheet: 0.44 (0.20), residues: 645 loop : -0.23 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 729 TYR 0.024 0.002 TYR C 108 PHE 0.023 0.002 PHE D 224 TRP 0.014 0.002 TRP A 280 HIS 0.007 0.002 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00764 (16934) covalent geometry : angle 0.62744 (22964) SS BOND : bond 0.00336 ( 17) SS BOND : angle 0.98942 ( 34) hydrogen bonds : bond 0.03752 ( 546) hydrogen bonds : angle 5.42340 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8285 (t0) cc_final: 0.7484 (p0) REVERT: A 675 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8417 (mtp-110) REVERT: B 97 ARG cc_start: 0.8524 (ttp-110) cc_final: 0.8185 (ttp-110) REVERT: B 130 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8412 (mmtt) REVERT: B 407 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8064 (tpt) REVERT: B 508 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 520 ASP cc_start: 0.9033 (m-30) cc_final: 0.8174 (p0) REVERT: B 541 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: B 560 PHE cc_start: 0.8574 (m-80) cc_final: 0.8167 (m-80) REVERT: B 584 LYS cc_start: 0.8119 (tttt) cc_final: 0.7880 (tptp) REVERT: B 645 SER cc_start: 0.8917 (m) cc_final: 0.8343 (p) REVERT: B 680 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7575 (tpt) REVERT: C 171 LYS cc_start: 0.8617 (mttt) cc_final: 0.8306 (mmmt) REVERT: D 69 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7857 (mtp180) REVERT: D 272 ASN cc_start: 0.6104 (m-40) cc_final: 0.5760 (m-40) outliers start: 30 outliers final: 19 residues processed: 159 average time/residue: 0.1699 time to fit residues: 38.1656 Evaluate side-chains 156 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 550 ILE Chi-restraints excluded: chain B residue 680 MET Chi-restraints excluded: chain B residue 725 GLN Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 244 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 53 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 542 ASN B 703 HIS B 725 GLN C 229 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN D 244 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.079080 restraints weight = 28271.230| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.63 r_work: 0.2867 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16951 Z= 0.129 Angle : 0.523 21.572 22998 Z= 0.272 Chirality : 0.044 0.222 2444 Planarity : 0.005 0.181 2988 Dihedral : 4.771 56.722 2271 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 0.99 % Allowed : 11.20 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2050 helix: 0.38 (0.36), residues: 202 sheet: 0.49 (0.20), residues: 649 loop : -0.12 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 729 TYR 0.023 0.001 TYR C 108 PHE 0.022 0.001 PHE D 224 TRP 0.012 0.001 TRP A 280 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00296 (16934) covalent geometry : angle 0.52243 (22964) SS BOND : bond 0.00191 ( 17) SS BOND : angle 0.96591 ( 34) hydrogen bonds : bond 0.02964 ( 546) hydrogen bonds : angle 5.13180 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8167 (t0) cc_final: 0.7317 (p0) REVERT: A 675 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8342 (mtp-110) REVERT: B 97 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8175 (ttp-110) REVERT: B 130 LYS cc_start: 0.8879 (mmmm) cc_final: 0.8315 (mmtt) REVERT: B 407 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7724 (tpt) REVERT: B 408 TYR cc_start: 0.8516 (m-80) cc_final: 0.8253 (m-80) REVERT: B 508 ASN cc_start: 0.8892 (p0) cc_final: 0.8354 (t0) REVERT: B 520 ASP cc_start: 0.8936 (m-30) cc_final: 0.8060 (p0) REVERT: B 541 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7143 (ttm-80) REVERT: B 560 PHE cc_start: 0.8458 (m-80) cc_final: 0.8116 (m-80) REVERT: B 584 LYS cc_start: 0.8041 (tttt) cc_final: 0.7720 (tptp) REVERT: B 645 SER cc_start: 0.8903 (m) cc_final: 0.8303 (p) REVERT: C 171 LYS cc_start: 0.8644 (mttt) cc_final: 0.8337 (mmmt) REVERT: D 69 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7774 (mtp180) REVERT: D 272 ASN cc_start: 0.6049 (m-40) cc_final: 0.5704 (m-40) outliers start: 18 outliers final: 14 residues processed: 150 average time/residue: 0.1793 time to fit residues: 37.9171 Evaluate side-chains 150 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 chunk 148 optimal weight: 0.0020 chunk 46 optimal weight: 0.0980 chunk 92 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN C 229 GLN C 254 GLN D 113 ASN D 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.124977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.079147 restraints weight = 28222.381| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.62 r_work: 0.2865 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16951 Z= 0.143 Angle : 0.518 20.196 22998 Z= 0.269 Chirality : 0.044 0.213 2444 Planarity : 0.005 0.176 2988 Dihedral : 4.606 54.961 2269 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 1.21 % Allowed : 11.03 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.18), residues: 2050 helix: 0.42 (0.35), residues: 204 sheet: 0.53 (0.20), residues: 643 loop : -0.08 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 729 TYR 0.020 0.001 TYR C 108 PHE 0.023 0.001 PHE D 224 TRP 0.011 0.001 TRP A 280 HIS 0.004 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00332 (16934) covalent geometry : angle 0.51722 (22964) SS BOND : bond 0.00203 ( 17) SS BOND : angle 0.85323 ( 34) hydrogen bonds : bond 0.02936 ( 546) hydrogen bonds : angle 5.07050 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5529.62 seconds wall clock time: 95 minutes 27.53 seconds (5727.53 seconds total)