Starting phenix.real_space_refine on Sun May 18 05:45:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cmt_16745/05_2025/8cmt_16745_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cmt_16745/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cmt_16745/05_2025/8cmt_16745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cmt_16745/05_2025/8cmt_16745.map" model { file = "/net/cci-nas-00/data/ceres_data/8cmt_16745/05_2025/8cmt_16745_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cmt_16745/05_2025/8cmt_16745_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.86, per 1000 atoms: 0.72 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: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.42 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: 5.76 Time building geometry restraints manager: 4.14 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: 0.010 Normalize map: mean=0, sd=1: 7.250 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.830 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (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 TRP 0.114 0.021 TRP A 316 HIS 0.010 0.003 HIS B 343 PHE 0.066 0.014 PHE A 608 TYR 0.138 0.018 TYR B 284 ARG 0.018 0.001 ARG A 516 Details of bonding type rmsd hydrogen bonds : bond 0.13398 ( 546) hydrogen bonds : angle 8.12509 ( 1500) SS BOND : bond 0.00737 ( 17) SS BOND : angle 1.18961 ( 34) covalent geometry : bond 0.01240 (16934) covalent geometry : angle 1.74395 (22964) *********************** 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 : 1.955 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: 0.7809 (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: 0.7985 (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: 0.8370 (mmt-90) REVERT: D 93 LYS cc_start: 0.7951 (tttt) cc_final: 0.7678 (ttmt) outliers start: 33 outliers final: 5 residues processed: 347 average time/residue: 0.4168 time to fit residues: 194.2431 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 : 1.916 ------------------------------------------------------------------------------- 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 172 optimal weight: 0.0570 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 185 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 543 ASN B 725 GLN C 37 GLN C 73 GLN ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3833 r_free = 0.3833 target = 0.130496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083325 restraints weight = 28767.624| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.59 r_work: 0.3013 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16951 Z= 0.136 Angle : 0.590 14.163 22998 Z= 0.318 Chirality : 0.046 0.253 2444 Planarity : 0.006 0.169 2988 Dihedral : 5.942 59.819 2282 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.56 % Favored : 98.34 % Rotamer: Outliers : 1.37 % Allowed : 7.79 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2050 helix: 0.19 (0.34), residues: 196 sheet: 0.86 (0.20), residues: 640 loop : 0.12 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 280 HIS 0.006 0.001 HIS B 703 PHE 0.022 0.002 PHE D 224 TYR 0.012 0.001 TYR C 116 ARG 0.006 0.001 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 546) hydrogen bonds : angle 5.94684 ( 1500) SS BOND : bond 0.00200 ( 17) SS BOND : angle 1.15445 ( 34) covalent geometry : bond 0.00311 (16934) covalent geometry : angle 0.58828 (22964) *********************** 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 212 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8244 (t0) cc_final: 0.7668 (p0) REVERT: A 286 TYR cc_start: 0.8438 (m-80) cc_final: 0.8197 (m-80) REVERT: A 521 MET cc_start: 0.8594 (ttp) cc_final: 0.8220 (ttp) REVERT: A 571 LYS cc_start: 0.8964 (ttpp) cc_final: 0.8742 (ptpt) REVERT: A 612 ARG cc_start: 0.7976 (ptm160) cc_final: 0.7473 (ptm160) REVERT: A 618 ASP cc_start: 0.7889 (m-30) cc_final: 0.7682 (m-30) REVERT: A 658 LYS cc_start: 0.7817 (mmpt) cc_final: 0.6941 (mtmm) REVERT: A 675 ARG cc_start: 0.8865 (mtm-85) cc_final: 0.8468 (mtp-110) REVERT: B 43 GLN cc_start: 0.7696 (mp10) cc_final: 0.7434 (mp10) REVERT: B 130 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8107 (mptt) REVERT: B 476 MET cc_start: 0.8701 (ttm) cc_final: 0.8338 (ttt) REVERT: B 491 GLU cc_start: 0.8369 (tt0) cc_final: 0.8075 (tt0) REVERT: B 520 ASP cc_start: 0.8580 (m-30) cc_final: 0.7870 (p0) REVERT: B 541 ARG cc_start: 0.7721 (ttm-80) cc_final: 0.7238 (ttm110) REVERT: B 584 LYS cc_start: 0.8609 (tttt) cc_final: 0.8231 (tptt) REVERT: B 596 MET cc_start: 0.8589 (mmm) cc_final: 0.8280 (mmm) REVERT: B 615 GLU cc_start: 0.8118 (mp0) cc_final: 0.7783 (mp0) REVERT: B 645 SER cc_start: 0.9127 (m) cc_final: 0.8736 (p) REVERT: B 677 MET cc_start: 0.7761 (mtt) cc_final: 0.7445 (mtt) REVERT: B 687 ASN cc_start: 0.8322 (m-40) cc_final: 0.7895 (p0) REVERT: B 697 ARG cc_start: 0.8918 (ttm-80) cc_final: 0.8679 (mtp85) REVERT: C 108 TYR cc_start: 0.8073 (m-80) cc_final: 0.7835 (m-80) REVERT: C 143 GLN cc_start: 0.8056 (tp-100) cc_final: 0.7829 (tp40) REVERT: C 229 GLN cc_start: 0.6782 (mm-40) cc_final: 0.6554 (mp10) REVERT: D 29 HIS cc_start: 0.8008 (t-90) cc_final: 0.7712 (t-90) REVERT: D 93 LYS cc_start: 0.8102 (tttt) cc_final: 0.7822 (ttmt) REVERT: D 272 ASN cc_start: 0.6008 (m-40) cc_final: 0.5764 (m-40) outliers start: 25 outliers final: 10 residues processed: 202 average time/residue: 0.3666 time to fit residues: 103.5746 Evaluate side-chains 161 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 525 VAL Chi-restraints excluded: chain B residue 529 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 240 PHE Chi-restraints excluded: chain D residue 244 ASN 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 110 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 164 optimal weight: 0.0010 chunk 6 optimal weight: 0.7980 chunk 190 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 198 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.127276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.081507 restraints weight = 28613.345| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.56 r_work: 0.2924 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16951 Z= 0.108 Angle : 0.512 13.737 22998 Z= 0.273 Chirality : 0.044 0.234 2444 Planarity : 0.005 0.165 2988 Dihedral : 5.052 57.990 2273 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.00 % Rotamer: Outliers : 1.26 % Allowed : 8.34 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2050 helix: 0.54 (0.35), residues: 198 sheet: 0.94 (0.20), residues: 643 loop : 0.18 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.004 0.001 HIS D 225 PHE 0.023 0.002 PHE D 224 TYR 0.012 0.001 TYR C 246 ARG 0.011 0.001 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 546) hydrogen bonds : angle 5.30747 ( 1500) SS BOND : bond 0.00172 ( 17) SS BOND : angle 1.20106 ( 34) covalent geometry : bond 0.00242 (16934) covalent geometry : angle 0.51001 (22964) *********************** 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 191 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 VAL cc_start: 0.9263 (m) cc_final: 0.9059 (p) REVERT: A 141 ARG cc_start: 0.8317 (mmt90) cc_final: 0.7738 (mmt90) REVERT: A 286 TYR cc_start: 0.8525 (m-80) cc_final: 0.8288 (m-80) REVERT: A 364 LYS cc_start: 0.8756 (mppt) cc_final: 0.8427 (mptt) REVERT: A 521 MET cc_start: 0.8669 (ttp) cc_final: 0.8343 (ttp) REVERT: A 571 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8735 (ptpt) REVERT: A 658 LYS cc_start: 0.7895 (mmpt) cc_final: 0.6952 (mtmm) REVERT: A 669 ASP cc_start: 0.8645 (t0) cc_final: 0.8381 (t0) REVERT: A 675 ARG cc_start: 0.8784 (mtm-85) cc_final: 0.8395 (mtp-110) REVERT: B 43 GLN cc_start: 0.7721 (mp10) cc_final: 0.7511 (mp10) REVERT: B 130 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8184 (mptt) REVERT: B 360 ASN cc_start: 0.8151 (t0) cc_final: 0.7944 (t0) REVERT: B 476 MET cc_start: 0.8672 (ttm) cc_final: 0.8287 (ttt) REVERT: B 513 MET cc_start: 0.8171 (mmt) cc_final: 0.7948 (mmt) REVERT: B 520 ASP cc_start: 0.8605 (m-30) cc_final: 0.7737 (p0) REVERT: B 541 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.7247 (ttm110) REVERT: B 584 LYS cc_start: 0.8561 (tttt) cc_final: 0.8056 (tptt) REVERT: B 596 MET cc_start: 0.8519 (mmm) cc_final: 0.8206 (mmm) REVERT: B 645 SER cc_start: 0.9073 (m) cc_final: 0.8787 (p) REVERT: B 687 ASN cc_start: 0.8484 (m-40) cc_final: 0.8020 (p0) REVERT: B 697 ARG cc_start: 0.8925 (ttm-80) cc_final: 0.8388 (mtp85) REVERT: C 143 GLN cc_start: 0.8023 (tp-100) cc_final: 0.7766 (tp-100) REVERT: C 171 LYS cc_start: 0.8575 (mttt) cc_final: 0.8269 (mmmt) REVERT: C 272 ASN cc_start: 0.7403 (m110) cc_final: 0.6994 (m110) REVERT: D 29 HIS cc_start: 0.8032 (t-90) cc_final: 0.7705 (t-90) REVERT: D 93 LYS cc_start: 0.7944 (tttt) cc_final: 0.7700 (ttmt) REVERT: D 272 ASN cc_start: 0.6138 (m-40) cc_final: 0.5855 (m-40) outliers start: 23 outliers final: 11 residues processed: 179 average time/residue: 0.3592 time to fit residues: 90.9470 Evaluate side-chains 158 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 560 PHE 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 250 SER Chi-restraints excluded: chain D residue 169 THR 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 90 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 606 HIS B 703 HIS ** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 ASN ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076555 restraints weight = 29077.789| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.55 r_work: 0.2829 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16951 Z= 0.301 Angle : 0.620 17.527 22998 Z= 0.328 Chirality : 0.048 0.194 2444 Planarity : 0.005 0.175 2988 Dihedral : 5.083 56.701 2269 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 1.54 % Allowed : 8.95 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2050 helix: -0.18 (0.34), residues: 214 sheet: 0.65 (0.20), residues: 649 loop : 0.02 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 280 HIS 0.005 0.001 HIS A 65 PHE 0.029 0.002 PHE D 224 TYR 0.018 0.002 TYR B 284 ARG 0.006 0.001 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 546) hydrogen bonds : angle 5.60275 ( 1500) SS BOND : bond 0.00354 ( 17) SS BOND : angle 1.25200 ( 34) covalent geometry : bond 0.00713 (16934) covalent geometry : angle 0.61901 (22964) *********************** 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 178 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8411 (mmt90) cc_final: 0.7467 (mmt90) REVERT: A 217 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7693 (pp20) REVERT: A 220 ASP cc_start: 0.8352 (t0) cc_final: 0.7624 (p0) REVERT: A 273 GLU cc_start: 0.8143 (tp30) cc_final: 0.7911 (mm-30) REVERT: A 286 TYR cc_start: 0.8454 (m-80) cc_final: 0.8224 (m-80) REVERT: A 407 MET cc_start: 0.9195 (tpt) cc_final: 0.8684 (tpt) REVERT: A 521 MET cc_start: 0.8769 (ttp) cc_final: 0.8557 (ttp) REVERT: A 675 ARG cc_start: 0.8803 (mtm-85) cc_final: 0.8459 (mtp-110) REVERT: A 677 MET cc_start: 0.7050 (mtt) cc_final: 0.6832 (mtt) REVERT: B 130 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8572 (mptt) REVERT: B 360 ASN cc_start: 0.8086 (t0) cc_final: 0.7830 (t0) REVERT: B 407 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8195 (tpt) REVERT: B 508 ASN cc_start: 0.8946 (p0) cc_final: 0.8454 (t0) REVERT: B 520 ASP cc_start: 0.8900 (m-30) cc_final: 0.7983 (p0) REVERT: B 541 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7177 (ttm110) REVERT: B 584 LYS cc_start: 0.8342 (tttt) cc_final: 0.7834 (tptt) REVERT: B 596 MET cc_start: 0.8596 (mmm) cc_final: 0.8283 (tpt) REVERT: B 645 SER cc_start: 0.8989 (m) cc_final: 0.8446 (p) REVERT: B 687 ASN cc_start: 0.8717 (m-40) cc_final: 0.8240 (p0) REVERT: C 246 TYR cc_start: 0.7184 (m-80) cc_final: 0.6933 (m-80) REVERT: D 69 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7931 (mtp180) REVERT: D 272 ASN cc_start: 0.6096 (m-40) cc_final: 0.5792 (m-40) outliers start: 28 outliers final: 15 residues processed: 169 average time/residue: 0.3361 time to fit residues: 81.6727 Evaluate side-chains 148 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 439 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 C residue 328 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 20 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 39 optimal weight: 0.0070 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 HIS B 703 HIS C 254 GLN D 113 ASN D 242 HIS ** D 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081866 restraints weight = 28775.901| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.47 r_work: 0.2943 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16951 Z= 0.147 Angle : 0.511 17.360 22998 Z= 0.268 Chirality : 0.044 0.240 2444 Planarity : 0.005 0.172 2988 Dihedral : 4.746 59.986 2269 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 1.10 % Allowed : 9.39 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2050 helix: 0.27 (0.35), residues: 204 sheet: 0.70 (0.20), residues: 647 loop : 0.04 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 280 HIS 0.002 0.001 HIS B 667 PHE 0.022 0.002 PHE D 224 TYR 0.017 0.001 TYR D 292 ARG 0.005 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 546) hydrogen bonds : angle 5.21252 ( 1500) SS BOND : bond 0.00218 ( 17) SS BOND : angle 1.12132 ( 34) covalent geometry : bond 0.00343 (16934) covalent geometry : angle 0.50950 (22964) *********************** 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 168 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8507 (mmt90) cc_final: 0.7559 (mmt90) REVERT: A 220 ASP cc_start: 0.8294 (t0) cc_final: 0.7549 (p0) REVERT: A 286 TYR cc_start: 0.8429 (m-80) cc_final: 0.8217 (m-80) REVERT: A 521 MET cc_start: 0.8737 (ttp) cc_final: 0.8526 (ttp) REVERT: A 669 ASP cc_start: 0.8668 (t70) cc_final: 0.8463 (t0) REVERT: A 675 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8468 (mtp-110) REVERT: A 677 MET cc_start: 0.7140 (mtt) cc_final: 0.6893 (mtt) REVERT: B 97 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7745 (ttp-110) REVERT: B 130 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8420 (mptt) REVERT: B 196 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 360 ASN cc_start: 0.8081 (t0) cc_final: 0.7808 (t0) REVERT: B 508 ASN cc_start: 0.8908 (p0) cc_final: 0.8446 (t0) REVERT: B 520 ASP cc_start: 0.8860 (m-30) cc_final: 0.7994 (p0) REVERT: B 541 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7128 (ttm110) REVERT: B 645 SER cc_start: 0.9006 (m) cc_final: 0.8485 (p) REVERT: B 687 ASN cc_start: 0.8660 (m-40) cc_final: 0.8224 (p0) REVERT: C 108 TYR cc_start: 0.8109 (m-80) cc_final: 0.7900 (m-80) REVERT: C 246 TYR cc_start: 0.7463 (m-80) cc_final: 0.7240 (m-80) REVERT: D 69 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7922 (mtp180) REVERT: D 272 ASN cc_start: 0.6119 (m-40) cc_final: 0.5796 (m-40) outliers start: 20 outliers final: 15 residues processed: 160 average time/residue: 0.3406 time to fit residues: 77.9138 Evaluate side-chains 153 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 137 MET Chi-restraints excluded: chain B residue 196 LEU 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 113 ASN Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 623 GLN B 703 HIS C 254 GLN D 242 HIS 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 = 0.3749 r_free = 0.3749 target = 0.126102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.079599 restraints weight = 28565.641| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.62 r_work: 0.2898 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16951 Z= 0.132 Angle : 0.504 19.015 22998 Z= 0.263 Chirality : 0.044 0.233 2444 Planarity : 0.005 0.177 2988 Dihedral : 4.577 57.775 2269 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 1.37 % Allowed : 9.60 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.18), residues: 2050 helix: 0.45 (0.35), residues: 204 sheet: 0.68 (0.20), residues: 645 loop : 0.08 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 280 HIS 0.004 0.001 HIS D 242 PHE 0.021 0.001 PHE D 224 TYR 0.016 0.001 TYR D 292 ARG 0.005 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 546) hydrogen bonds : angle 5.06355 ( 1500) SS BOND : bond 0.00606 ( 17) SS BOND : angle 1.12314 ( 34) covalent geometry : bond 0.00304 (16934) covalent geometry : angle 0.50264 (22964) *********************** 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 166 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8478 (mmt90) cc_final: 0.7502 (mmt90) REVERT: A 220 ASP cc_start: 0.8220 (t0) cc_final: 0.7401 (p0) REVERT: A 286 TYR cc_start: 0.8467 (m-80) cc_final: 0.8236 (m-80) REVERT: A 513 MET cc_start: 0.6284 (tpp) cc_final: 0.5987 (tpp) REVERT: A 521 MET cc_start: 0.8763 (ttp) cc_final: 0.8537 (ttp) REVERT: A 669 ASP cc_start: 0.8727 (t70) cc_final: 0.8518 (t0) REVERT: A 675 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8372 (mtp-110) REVERT: A 677 MET cc_start: 0.6946 (mtt) cc_final: 0.6615 (mtt) REVERT: B 97 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7971 (ttp-110) REVERT: B 130 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8443 (mptt) REVERT: B 196 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8978 (tt) REVERT: B 360 ASN cc_start: 0.7971 (t0) cc_final: 0.7675 (t0) REVERT: B 408 TYR cc_start: 0.8468 (m-80) cc_final: 0.8134 (m-80) REVERT: B 508 ASN cc_start: 0.8889 (p0) cc_final: 0.8341 (t0) REVERT: B 520 ASP cc_start: 0.8853 (m-30) cc_final: 0.7950 (p0) REVERT: B 521 MET cc_start: 0.9287 (ppp) cc_final: 0.9063 (ppp) REVERT: B 541 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7067 (ttm110) REVERT: B 584 LYS cc_start: 0.8234 (tttt) cc_final: 0.7929 (tptp) REVERT: B 645 SER cc_start: 0.8952 (m) cc_final: 0.8360 (p) REVERT: B 680 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7454 (tpt) REVERT: B 687 ASN cc_start: 0.8761 (m-40) cc_final: 0.8242 (p0) REVERT: C 108 TYR cc_start: 0.8116 (m-80) cc_final: 0.7890 (m-80) REVERT: C 171 LYS cc_start: 0.8617 (mttt) cc_final: 0.8314 (mmmt) REVERT: C 246 TYR cc_start: 0.7564 (m-80) cc_final: 0.7272 (m-80) REVERT: C 261 TYR cc_start: 0.6168 (t80) cc_final: 0.5803 (t80) REVERT: D 69 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7870 (mtp180) REVERT: D 272 ASN cc_start: 0.6070 (m-40) cc_final: 0.5752 (m-40) outliers start: 25 outliers final: 17 residues processed: 155 average time/residue: 0.3446 time to fit residues: 75.9851 Evaluate side-chains 153 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 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 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 328 ILE Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 287 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 198 optimal weight: 30.0000 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 186 optimal weight: 0.0030 chunk 105 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 A 623 GLN B 703 HIS C 37 GLN C 254 GLN D 113 ASN D 244 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 = 0.3760 r_free = 0.3760 target = 0.126822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.081089 restraints weight = 28535.562| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.62 r_work: 0.2922 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16951 Z= 0.102 Angle : 0.486 19.997 22998 Z= 0.251 Chirality : 0.043 0.239 2444 Planarity : 0.005 0.178 2988 Dihedral : 4.366 53.485 2269 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.10 % Allowed : 10.37 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2050 helix: 0.65 (0.36), residues: 204 sheet: 0.78 (0.20), residues: 643 loop : 0.10 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 376 HIS 0.002 0.001 HIS A 422 PHE 0.020 0.001 PHE D 224 TYR 0.020 0.001 TYR D 292 ARG 0.005 0.000 ARG B 617 Details of bonding type rmsd hydrogen bonds : bond 0.02642 ( 546) hydrogen bonds : angle 4.87531 ( 1500) SS BOND : bond 0.00204 ( 17) SS BOND : angle 1.06278 ( 34) covalent geometry : bond 0.00233 (16934) covalent geometry : angle 0.48417 (22964) *********************** 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 165 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8489 (mmt90) cc_final: 0.7560 (mmt90) REVERT: A 220 ASP cc_start: 0.8211 (t0) cc_final: 0.7356 (p0) REVERT: A 286 TYR cc_start: 0.8450 (m-80) cc_final: 0.8223 (m-80) REVERT: A 521 MET cc_start: 0.8792 (ttp) cc_final: 0.8553 (ttp) REVERT: A 669 ASP cc_start: 0.8649 (t70) cc_final: 0.8444 (t0) REVERT: A 675 ARG cc_start: 0.8675 (mtm-85) cc_final: 0.8312 (mtp-110) REVERT: A 677 MET cc_start: 0.6976 (mtt) cc_final: 0.6477 (mtt) REVERT: B 97 ARG cc_start: 0.8284 (ttp-110) cc_final: 0.7983 (ttp-110) REVERT: B 130 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8228 (mmtt) REVERT: B 196 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8908 (tt) REVERT: B 360 ASN cc_start: 0.7936 (t0) cc_final: 0.7655 (t0) REVERT: B 407 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7892 (tpt) REVERT: B 408 TYR cc_start: 0.8402 (m-80) cc_final: 0.8026 (m-80) REVERT: B 508 ASN cc_start: 0.8846 (p0) cc_final: 0.8246 (t0) REVERT: B 520 ASP cc_start: 0.8809 (m-30) cc_final: 0.7939 (p0) REVERT: B 541 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7059 (ttm110) REVERT: B 584 LYS cc_start: 0.8179 (tttt) cc_final: 0.7904 (tptp) REVERT: B 645 SER cc_start: 0.8960 (m) cc_final: 0.8355 (p) REVERT: B 680 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7427 (tpt) REVERT: B 687 ASN cc_start: 0.8755 (m-40) cc_final: 0.8215 (p0) REVERT: C 108 TYR cc_start: 0.8150 (m-80) cc_final: 0.7932 (m-80) REVERT: C 171 LYS cc_start: 0.8677 (mttt) cc_final: 0.8366 (mmmt) REVERT: C 246 TYR cc_start: 0.7690 (m-80) cc_final: 0.7407 (m-80) REVERT: D 69 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7899 (mtp180) REVERT: D 272 ASN cc_start: 0.6007 (m-40) cc_final: 0.5691 (m-40) outliers start: 20 outliers final: 14 residues processed: 154 average time/residue: 0.3766 time to fit residues: 82.8986 Evaluate side-chains 156 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL 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 680 MET 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 113 ASN Chi-restraints excluded: chain D residue 114 MET 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 157 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.3980 chunk 11 optimal weight: 0.2980 chunk 177 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080577 restraints weight = 28412.314| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.62 r_work: 0.2919 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16951 Z= 0.120 Angle : 0.493 21.398 22998 Z= 0.254 Chirality : 0.043 0.238 2444 Planarity : 0.005 0.182 2988 Dihedral : 4.341 52.137 2269 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.15 % Allowed : 10.32 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 2050 helix: 0.56 (0.36), residues: 208 sheet: 0.83 (0.21), residues: 633 loop : 0.11 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 376 HIS 0.003 0.001 HIS B 703 PHE 0.022 0.001 PHE D 224 TYR 0.022 0.001 TYR D 292 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 546) hydrogen bonds : angle 4.85793 ( 1500) SS BOND : bond 0.00197 ( 17) SS BOND : angle 1.06679 ( 34) covalent geometry : bond 0.00278 (16934) covalent geometry : angle 0.49176 (22964) *********************** 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 157 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8242 (t0) cc_final: 0.7401 (p0) REVERT: A 286 TYR cc_start: 0.8436 (m-80) cc_final: 0.8211 (m-80) REVERT: A 521 MET cc_start: 0.8783 (ttp) cc_final: 0.8547 (ttp) REVERT: A 675 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8338 (mtp-110) REVERT: A 677 MET cc_start: 0.7043 (mtt) cc_final: 0.6603 (mtt) REVERT: B 97 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.8008 (ttp-110) REVERT: B 130 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8274 (mmtt) REVERT: B 196 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 360 ASN cc_start: 0.7987 (t0) cc_final: 0.7698 (t0) REVERT: B 407 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7834 (tpt) REVERT: B 408 TYR cc_start: 0.8425 (m-80) cc_final: 0.8049 (m-80) REVERT: B 508 ASN cc_start: 0.8858 (p0) cc_final: 0.8238 (t0) REVERT: B 520 ASP cc_start: 0.8824 (m-30) cc_final: 0.7962 (p0) REVERT: B 541 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7084 (ttm110) REVERT: B 584 LYS cc_start: 0.8192 (tttt) cc_final: 0.7915 (tptp) REVERT: B 645 SER cc_start: 0.8954 (m) cc_final: 0.8353 (p) REVERT: B 680 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7445 (tpt) REVERT: B 687 ASN cc_start: 0.8760 (m-40) cc_final: 0.8195 (p0) REVERT: C 108 TYR cc_start: 0.8204 (m-80) cc_final: 0.8002 (m-80) REVERT: C 246 TYR cc_start: 0.7777 (m-80) cc_final: 0.7457 (m-80) REVERT: D 69 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7938 (mtp180) REVERT: D 272 ASN cc_start: 0.6034 (m-40) cc_final: 0.5722 (m-40) outliers start: 21 outliers final: 13 residues processed: 147 average time/residue: 0.3546 time to fit residues: 74.6041 Evaluate side-chains 149 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 30 VAL 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 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 C residue 328 ILE Chi-restraints excluded: chain D residue 114 MET 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 2 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 14 optimal weight: 0.0570 chunk 172 optimal weight: 40.0000 chunk 93 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 703 HIS C 254 GLN D 113 ASN 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 = 0.3739 r_free = 0.3739 target = 0.125430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079021 restraints weight = 28592.370| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.61 r_work: 0.2886 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16951 Z= 0.182 Angle : 0.521 18.236 22998 Z= 0.272 Chirality : 0.045 0.217 2444 Planarity : 0.005 0.171 2988 Dihedral : 4.471 52.717 2269 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Rotamer: Outliers : 1.32 % Allowed : 10.37 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2050 helix: 0.40 (0.36), residues: 208 sheet: 0.78 (0.21), residues: 631 loop : 0.02 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 280 HIS 0.004 0.001 HIS B 703 PHE 0.023 0.002 PHE D 224 TYR 0.020 0.001 TYR D 292 ARG 0.005 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 546) hydrogen bonds : angle 4.97523 ( 1500) SS BOND : bond 0.00215 ( 17) SS BOND : angle 1.00754 ( 34) covalent geometry : bond 0.00427 (16934) covalent geometry : angle 0.51980 (22964) *********************** 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 163 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8235 (t0) cc_final: 0.7393 (p0) REVERT: A 286 TYR cc_start: 0.8427 (m-80) cc_final: 0.8202 (m-80) REVERT: A 521 MET cc_start: 0.8794 (ttp) cc_final: 0.8554 (ttp) REVERT: A 675 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8358 (mtp-110) REVERT: A 677 MET cc_start: 0.7063 (mtt) cc_final: 0.6568 (mtt) REVERT: B 97 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.8029 (ttp-110) REVERT: B 130 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8334 (mmtt) REVERT: B 196 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8981 (tt) REVERT: B 360 ASN cc_start: 0.7987 (t0) cc_final: 0.7691 (t0) REVERT: B 407 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7862 (tpt) REVERT: B 408 TYR cc_start: 0.8470 (m-80) cc_final: 0.8166 (m-80) REVERT: B 508 ASN cc_start: 0.8897 (p0) cc_final: 0.8275 (t0) REVERT: B 520 ASP cc_start: 0.8856 (m-30) cc_final: 0.8000 (p0) REVERT: B 541 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7068 (ttm110) REVERT: B 645 SER cc_start: 0.8924 (m) cc_final: 0.8320 (p) REVERT: B 680 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.7389 (tpt) REVERT: C 246 TYR cc_start: 0.7976 (m-80) cc_final: 0.7712 (m-80) REVERT: D 69 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7939 (mtp180) REVERT: D 272 ASN cc_start: 0.6081 (m-40) cc_final: 0.5746 (m-40) outliers start: 24 outliers final: 18 residues processed: 151 average time/residue: 0.3822 time to fit residues: 81.9680 Evaluate side-chains 154 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE 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 444 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 525 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 C residue 328 ILE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 114 MET 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 64 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 120 optimal weight: 0.5980 chunk 174 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 113 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 = 0.3758 r_free = 0.3758 target = 0.126772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080409 restraints weight = 28528.384| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.63 r_work: 0.2919 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16951 Z= 0.115 Angle : 0.501 22.878 22998 Z= 0.257 Chirality : 0.043 0.241 2444 Planarity : 0.005 0.186 2988 Dihedral : 4.367 49.772 2269 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 1.15 % Allowed : 10.59 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2050 helix: 0.51 (0.36), residues: 208 sheet: 0.84 (0.21), residues: 622 loop : 0.07 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 280 HIS 0.003 0.001 HIS D 242 PHE 0.022 0.001 PHE D 224 TYR 0.018 0.001 TYR D 292 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02735 ( 546) hydrogen bonds : angle 4.87769 ( 1500) SS BOND : bond 0.00164 ( 17) SS BOND : angle 0.99493 ( 34) covalent geometry : bond 0.00265 (16934) covalent geometry : angle 0.49970 (22964) ********************** 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 156 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ASP cc_start: 0.8245 (t0) cc_final: 0.7441 (p0) REVERT: A 286 TYR cc_start: 0.8430 (m-80) cc_final: 0.8214 (m-80) REVERT: A 675 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8358 (mtp-110) REVERT: A 677 MET cc_start: 0.7133 (mtt) cc_final: 0.6703 (mtt) REVERT: B 97 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.8011 (ttp-110) REVERT: B 130 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8347 (mmtt) REVERT: B 196 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8971 (tt) REVERT: B 360 ASN cc_start: 0.8027 (t0) cc_final: 0.7733 (t0) REVERT: B 407 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7879 (tpt) REVERT: B 408 TYR cc_start: 0.8418 (m-80) cc_final: 0.8114 (m-80) REVERT: B 508 ASN cc_start: 0.8872 (p0) cc_final: 0.8286 (t0) REVERT: B 520 ASP cc_start: 0.8840 (m-30) cc_final: 0.8069 (p0) REVERT: B 541 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7138 (ttm110) REVERT: B 584 LYS cc_start: 0.8149 (tttt) cc_final: 0.7815 (tptp) REVERT: B 645 SER cc_start: 0.8987 (m) cc_final: 0.8412 (p) REVERT: B 680 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7417 (tpt) REVERT: C 171 LYS cc_start: 0.8690 (mttt) cc_final: 0.8394 (mmmt) REVERT: C 246 TYR cc_start: 0.8034 (m-80) cc_final: 0.7773 (m-80) REVERT: D 69 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7972 (mtp180) REVERT: D 272 ASN cc_start: 0.6049 (m-40) cc_final: 0.5714 (m-40) outliers start: 21 outliers final: 17 residues processed: 145 average time/residue: 0.3933 time to fit residues: 81.4654 Evaluate side-chains 151 residues out of total 1822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 283 ILE 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 444 THR Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 525 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 C residue 328 ILE Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 240 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 103 optimal weight: 2.9990 chunk 174 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN C 254 GLN D 113 ASN 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 = 0.3753 r_free = 0.3753 target = 0.126957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080860 restraints weight = 28380.120| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.64 r_work: 0.2902 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16951 Z= 0.106 Angle : 0.471 9.382 22998 Z= 0.251 Chirality : 0.043 0.151 2444 Planarity : 0.004 0.102 2988 Dihedral : 4.397 68.066 2269 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Rotamer: Outliers : 1.15 % Allowed : 10.59 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.26 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 2050 helix: 0.57 (0.36), residues: 208 sheet: 0.87 (0.21), residues: 622 loop : 0.08 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 280 HIS 0.004 0.001 HIS B 703 PHE 0.024 0.001 PHE D 224 TYR 0.028 0.001 TYR D 292 ARG 0.006 0.000 ARG A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02650 ( 546) hydrogen bonds : angle 4.84914 ( 1500) SS BOND : bond 0.00153 ( 17) SS BOND : angle 0.93171 ( 34) covalent geometry : bond 0.00241 (16934) covalent geometry : angle 0.46953 (22964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11101.73 seconds wall clock time: 193 minutes 15.38 seconds (11595.38 seconds total)