Starting phenix.real_space_refine on Wed Nov 19 04:53:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dvy_8920/11_2025/6dvy_8920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dvy_8920/11_2025/6dvy_8920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dvy_8920/11_2025/6dvy_8920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dvy_8920/11_2025/6dvy_8920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dvy_8920/11_2025/6dvy_8920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dvy_8920/11_2025/6dvy_8920.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 124 5.16 5 B 8 2.79 5 C 13684 2.51 5 N 3452 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21008 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5218 Classifications: {'peptide': 641} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 623} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'FZ4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.04, per 1000 atoms: 0.24 Number of scatterers: 21008 At special positions: 0 Unit cell: (132.98, 132.98, 124.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 124 16.00 O 3740 8.00 N 3452 7.00 C 13684 6.00 B 8 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 794.7 milliseconds 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 60.5% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.526A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.093A pdb=" N HIS A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.660A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.407A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 210 through 214 removed outlier: 4.249A pdb=" N GLU A 214 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.627A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.565A pdb=" N ALA A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.956A pdb=" N ARG A 319 " --> pdb=" O ASP A 315 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.599A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.515A pdb=" N THR A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 460 removed outlier: 3.626A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 508 removed outlier: 3.558A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 500 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 520 through 541 removed outlier: 4.143A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.587A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.631A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 4.050A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.596A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.562A pdb=" N ALA A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 677 removed outlier: 3.500A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 707 removed outlier: 3.706A pdb=" N SER A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.526A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 4.092A pdb=" N HIS B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.660A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.407A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 210 through 214 removed outlier: 4.251A pdb=" N GLU B 214 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.627A pdb=" N VAL B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.565A pdb=" N ALA B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 315 through 328 removed outlier: 3.956A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 363 removed outlier: 3.600A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.515A pdb=" N THR B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 460 removed outlier: 3.626A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 508 removed outlier: 3.558A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 500 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 520 through 541 removed outlier: 4.142A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.586A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.631A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 585 removed outlier: 4.050A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 606 removed outlier: 3.596A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 634 removed outlier: 3.563A pdb=" N ALA B 628 " --> pdb=" O SER B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 677 removed outlier: 3.562A pdb=" N THR B 660 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 707 removed outlier: 3.706A pdb=" N SER B 688 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 130 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.526A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 4.093A pdb=" N HIS C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.660A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.408A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 210 through 214 removed outlier: 4.251A pdb=" N GLU C 214 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.627A pdb=" N VAL C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.566A pdb=" N ALA C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.956A pdb=" N ARG C 319 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 363 removed outlier: 3.600A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.515A pdb=" N THR C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 460 removed outlier: 3.626A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 removed outlier: 3.557A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C 500 " --> pdb=" O CYS C 496 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 515 Processing helix chain 'C' and resid 520 through 541 removed outlier: 4.141A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.587A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.631A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 585 removed outlier: 4.049A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 606 removed outlier: 3.595A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 634 removed outlier: 3.564A pdb=" N ALA C 628 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 677 removed outlier: 3.561A pdb=" N THR C 660 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 669 " --> pdb=" O THR C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 707 removed outlier: 3.706A pdb=" N SER C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.526A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 4.094A pdb=" N HIS D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.660A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.408A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 210 through 214 removed outlier: 4.249A pdb=" N GLU D 214 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.627A pdb=" N VAL D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.566A pdb=" N ALA D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 315 through 328 removed outlier: 3.956A pdb=" N ARG D 319 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 363 removed outlier: 3.600A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.514A pdb=" N THR D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 460 removed outlier: 3.626A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 508 removed outlier: 3.558A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 500 " --> pdb=" O CYS D 496 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 504 " --> pdb=" O LYS D 500 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 515 Processing helix chain 'D' and resid 520 through 541 removed outlier: 4.143A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.587A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.631A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 585 removed outlier: 4.050A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 606 removed outlier: 3.596A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 634 removed outlier: 3.563A pdb=" N ALA D 628 " --> pdb=" O SER D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 677 removed outlier: 3.562A pdb=" N THR D 660 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 669 " --> pdb=" O THR D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 707 removed outlier: 3.706A pdb=" N SER D 688 " --> pdb=" O VAL D 684 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.791A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.792A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.792A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.792A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 955 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6393 1.34 - 1.46: 4040 1.46 - 1.57: 10831 1.57 - 1.69: 4 1.69 - 1.81: 204 Bond restraints: 21472 Sorted by residual: bond pdb=" C ASP C 752 " pdb=" N PRO C 753 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.28e-02 6.10e+03 2.38e+01 bond pdb=" C ASP A 752 " pdb=" N PRO A 753 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.28e-02 6.10e+03 2.35e+01 bond pdb=" C ASP D 752 " pdb=" N PRO D 753 " ideal model delta sigma weight residual 1.335 1.397 -0.062 1.28e-02 6.10e+03 2.34e+01 bond pdb=" C ASP B 752 " pdb=" N PRO B 753 " ideal model delta sigma weight residual 1.335 1.396 -0.062 1.28e-02 6.10e+03 2.31e+01 bond pdb=" C TYR C 650 " pdb=" N PRO C 651 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.19e-02 7.06e+03 1.32e+01 ... (remaining 21467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 26780 2.13 - 4.27: 1826 4.27 - 6.40: 304 6.40 - 8.54: 106 8.54 - 10.67: 20 Bond angle restraints: 29036 Sorted by residual: angle pdb=" C CYS D 619 " pdb=" N SER D 620 " pdb=" CA SER D 620 " ideal model delta sigma weight residual 122.44 115.72 6.72 1.19e+00 7.06e-01 3.19e+01 angle pdb=" C CYS C 619 " pdb=" N SER C 620 " pdb=" CA SER C 620 " ideal model delta sigma weight residual 122.44 115.74 6.70 1.19e+00 7.06e-01 3.17e+01 angle pdb=" C CYS B 619 " pdb=" N SER B 620 " pdb=" CA SER B 620 " ideal model delta sigma weight residual 122.44 115.79 6.65 1.19e+00 7.06e-01 3.12e+01 angle pdb=" C TRP A 739 " pdb=" N THR A 740 " pdb=" CA THR A 740 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C TRP C 739 " pdb=" N THR C 740 " pdb=" CA THR C 740 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.11e+01 ... (remaining 29031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 12272 22.22 - 44.45: 480 44.45 - 66.67: 24 66.67 - 88.90: 28 88.90 - 111.12: 8 Dihedral angle restraints: 12812 sinusoidal: 5244 harmonic: 7568 Sorted by residual: dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ASP B 153 " pdb=" CA ASP B 153 " ideal model delta harmonic sigma weight residual -180.00 -139.63 -40.37 0 5.00e+00 4.00e-02 6.52e+01 dihedral pdb=" CA LEU D 152 " pdb=" C LEU D 152 " pdb=" N ASP D 153 " pdb=" CA ASP D 153 " ideal model delta harmonic sigma weight residual -180.00 -139.66 -40.34 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA LEU A 152 " pdb=" C LEU A 152 " pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta harmonic sigma weight residual -180.00 -139.66 -40.34 0 5.00e+00 4.00e-02 6.51e+01 ... (remaining 12809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2372 0.059 - 0.117: 776 0.117 - 0.176: 97 0.176 - 0.234: 34 0.234 - 0.293: 13 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CG LEU C 730 " pdb=" CB LEU C 730 " pdb=" CD1 LEU C 730 " pdb=" CD2 LEU C 730 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU B 730 " pdb=" CB LEU B 730 " pdb=" CD1 LEU B 730 " pdb=" CD2 LEU B 730 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU A 730 " pdb=" CB LEU A 730 " pdb=" CD1 LEU A 730 " pdb=" CD2 LEU A 730 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 3289 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 368 " 0.062 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO D 369 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 369 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 369 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 368 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A 369 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 368 " 0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO C 369 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " 0.052 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 72 2.39 - 3.02: 10598 3.02 - 3.64: 32313 3.64 - 4.27: 47166 4.27 - 4.90: 74554 Nonbonded interactions: 164703 Sorted by model distance: nonbonded pdb=" CZ ARG D 696 " pdb=" C05 FZ4 D 801 " model vdw 1.762 2.856 nonbonded pdb=" CZ ARG C 696 " pdb=" C05 FZ4 C 801 " model vdw 1.774 2.856 nonbonded pdb=" CZ ARG A 696 " pdb=" C05 FZ4 A 801 " model vdw 1.781 2.856 nonbonded pdb=" CZ ARG B 696 " pdb=" C05 FZ4 B 801 " model vdw 1.797 2.856 nonbonded pdb=" CD2 HIS C 426 " pdb=" C12 FZ4 C 801 " model vdw 2.249 3.560 ... (remaining 164698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.340 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.009 0.307 21476 Z= 0.544 Angle : 1.252 10.671 29036 Z= 0.711 Chirality : 0.059 0.293 3292 Planarity : 0.007 0.094 3616 Dihedral : 12.657 111.121 7900 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.78 % Allowed : 12.99 % Favored : 86.23 % Rotamer: Outliers : 0.88 % Allowed : 4.03 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.79 (0.11), residues: 2556 helix: -3.93 (0.07), residues: 1396 sheet: -1.69 (0.65), residues: 76 loop : -3.76 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 226 TYR 0.017 0.003 TYR C 650 PHE 0.043 0.004 PHE B 633 TRP 0.025 0.003 TRP D 481 HIS 0.011 0.002 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00803 (21472) covalent geometry : angle 1.25197 (29036) hydrogen bonds : bond 0.30247 ( 955) hydrogen bonds : angle 10.28743 ( 2805) Misc. bond : bond 0.29462 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 831 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 CYS cc_start: 0.8480 (t) cc_final: 0.8185 (t) REVERT: A 191 LEU cc_start: 0.9165 (mt) cc_final: 0.8827 (mt) REVERT: A 195 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7890 (mm-30) REVERT: A 200 LEU cc_start: 0.9303 (pp) cc_final: 0.9037 (pp) REVERT: A 209 THR cc_start: 0.8958 (p) cc_final: 0.8722 (t) REVERT: A 235 ILE cc_start: 0.8935 (mt) cc_final: 0.8593 (tt) REVERT: A 288 ASP cc_start: 0.8452 (t0) cc_final: 0.7529 (p0) REVERT: A 291 SER cc_start: 0.8611 (t) cc_final: 0.8347 (p) REVERT: A 293 ASP cc_start: 0.8418 (t0) cc_final: 0.7927 (t0) REVERT: A 336 MET cc_start: 0.8831 (ttm) cc_final: 0.8618 (ttm) REVERT: A 373 LEU cc_start: 0.8829 (mt) cc_final: 0.8112 (mt) REVERT: A 444 SER cc_start: 0.9139 (p) cc_final: 0.8673 (t) REVERT: A 479 MET cc_start: 0.7759 (mmm) cc_final: 0.7412 (mtp) REVERT: A 562 MET cc_start: 0.8481 (mmp) cc_final: 0.8274 (mmm) REVERT: A 572 MET cc_start: 0.8977 (tpt) cc_final: 0.8772 (tpp) REVERT: A 639 LEU cc_start: 0.7615 (tt) cc_final: 0.7332 (tt) REVERT: A 683 ASN cc_start: 0.8360 (m-40) cc_final: 0.7870 (m-40) REVERT: A 688 SER cc_start: 0.9428 (m) cc_final: 0.8840 (p) REVERT: B 171 CYS cc_start: 0.8503 (t) cc_final: 0.8182 (t) REVERT: B 195 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7927 (mm-30) REVERT: B 200 LEU cc_start: 0.9303 (pp) cc_final: 0.8630 (pp) REVERT: B 209 THR cc_start: 0.8971 (p) cc_final: 0.8715 (t) REVERT: B 235 ILE cc_start: 0.8985 (mt) cc_final: 0.8669 (tt) REVERT: B 265 PRO cc_start: 0.9350 (Cg_exo) cc_final: 0.9142 (Cg_endo) REVERT: B 288 ASP cc_start: 0.8460 (t0) cc_final: 0.7664 (p0) REVERT: B 291 SER cc_start: 0.8681 (t) cc_final: 0.8459 (p) REVERT: B 305 THR cc_start: 0.9186 (p) cc_final: 0.8961 (t) REVERT: B 373 LEU cc_start: 0.8813 (mt) cc_final: 0.8123 (mt) REVERT: B 444 SER cc_start: 0.9149 (p) cc_final: 0.8670 (t) REVERT: B 631 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 683 ASN cc_start: 0.8325 (m-40) cc_final: 0.7928 (m-40) REVERT: B 688 SER cc_start: 0.9359 (m) cc_final: 0.8746 (p) REVERT: C 171 CYS cc_start: 0.8505 (t) cc_final: 0.8217 (t) REVERT: C 191 LEU cc_start: 0.9156 (mt) cc_final: 0.8824 (mt) REVERT: C 195 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7875 (mm-30) REVERT: C 200 LEU cc_start: 0.9295 (pp) cc_final: 0.9013 (pp) REVERT: C 209 THR cc_start: 0.8912 (p) cc_final: 0.8679 (t) REVERT: C 235 ILE cc_start: 0.9014 (mt) cc_final: 0.8697 (tt) REVERT: C 288 ASP cc_start: 0.8519 (t0) cc_final: 0.7457 (p0) REVERT: C 291 SER cc_start: 0.8701 (t) cc_final: 0.8419 (p) REVERT: C 373 LEU cc_start: 0.8806 (mt) cc_final: 0.8046 (mt) REVERT: C 444 SER cc_start: 0.9154 (p) cc_final: 0.8676 (t) REVERT: C 639 LEU cc_start: 0.7463 (tt) cc_final: 0.6610 (tt) REVERT: C 683 ASN cc_start: 0.8358 (m-40) cc_final: 0.7868 (m-40) REVERT: C 688 SER cc_start: 0.9369 (m) cc_final: 0.8829 (p) REVERT: D 171 CYS cc_start: 0.8478 (t) cc_final: 0.8142 (t) REVERT: D 191 LEU cc_start: 0.9157 (mt) cc_final: 0.8814 (mt) REVERT: D 195 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7921 (mm-30) REVERT: D 200 LEU cc_start: 0.9272 (pp) cc_final: 0.9014 (pp) REVERT: D 209 THR cc_start: 0.8885 (p) cc_final: 0.8668 (t) REVERT: D 235 ILE cc_start: 0.9017 (mt) cc_final: 0.8587 (tt) REVERT: D 265 PRO cc_start: 0.9392 (Cg_exo) cc_final: 0.9191 (Cg_endo) REVERT: D 288 ASP cc_start: 0.8448 (t0) cc_final: 0.7307 (p0) REVERT: D 291 SER cc_start: 0.8651 (t) cc_final: 0.8364 (p) REVERT: D 293 ASP cc_start: 0.8378 (t0) cc_final: 0.7456 (t0) REVERT: D 373 LEU cc_start: 0.8836 (mt) cc_final: 0.8071 (mt) REVERT: D 444 SER cc_start: 0.9165 (p) cc_final: 0.8724 (t) REVERT: D 479 MET cc_start: 0.7733 (mmm) cc_final: 0.7333 (mtp) REVERT: D 562 MET cc_start: 0.8497 (mmp) cc_final: 0.8192 (mmm) REVERT: D 572 MET cc_start: 0.9026 (tpt) cc_final: 0.8762 (tpp) REVERT: D 683 ASN cc_start: 0.8387 (m-40) cc_final: 0.7855 (m-40) REVERT: D 688 SER cc_start: 0.9418 (m) cc_final: 0.8943 (p) outliers start: 20 outliers final: 4 residues processed: 851 average time/residue: 0.1572 time to fit residues: 206.5242 Evaluate side-chains 496 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 492 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain D residue 539 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0050 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 297 ASN A 330 ASN A 483 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 273 ASN B 297 ASN B 483 GLN B 645 GLN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 273 ASN C 297 ASN C 483 GLN C 645 GLN ** C 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 ASN D 297 ASN D 330 ASN D 483 GLN D 645 GLN ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099336 restraints weight = 48226.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.101939 restraints weight = 28950.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.103562 restraints weight = 20521.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104842 restraints weight = 16431.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105659 restraints weight = 14011.728| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21476 Z= 0.157 Angle : 0.873 14.169 29036 Z= 0.436 Chirality : 0.045 0.167 3292 Planarity : 0.006 0.073 3616 Dihedral : 9.243 82.355 2844 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.82 % Favored : 87.72 % Rotamer: Outliers : 4.73 % Allowed : 12.87 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.67 (0.14), residues: 2556 helix: -1.75 (0.11), residues: 1464 sheet: -1.42 (0.68), residues: 76 loop : -3.52 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 696 TYR 0.024 0.002 TYR A 451 PHE 0.027 0.002 PHE D 666 TRP 0.027 0.003 TRP A 710 HIS 0.010 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00337 (21472) covalent geometry : angle 0.87328 (29036) hydrogen bonds : bond 0.04620 ( 955) hydrogen bonds : angle 5.19282 ( 2805) Misc. bond : bond 0.00126 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 597 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: A 137 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8790 (mp0) REVERT: A 171 CYS cc_start: 0.8424 (t) cc_final: 0.8119 (t) REVERT: A 209 THR cc_start: 0.8743 (p) cc_final: 0.8496 (t) REVERT: A 282 MET cc_start: 0.8229 (mtp) cc_final: 0.7863 (mmm) REVERT: A 336 MET cc_start: 0.8718 (ttm) cc_final: 0.8463 (ttm) REVERT: A 346 GLN cc_start: 0.8678 (mt0) cc_final: 0.8079 (mt0) REVERT: A 430 HIS cc_start: 0.8624 (t-90) cc_final: 0.8315 (t70) REVERT: A 446 CYS cc_start: 0.8637 (m) cc_final: 0.8235 (m) REVERT: A 501 GLU cc_start: 0.8402 (mp0) cc_final: 0.8056 (mp0) REVERT: A 529 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8516 (tm-30) REVERT: A 631 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7394 (tp30) REVERT: A 702 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 710 TRP cc_start: 0.7381 (p-90) cc_final: 0.7100 (p-90) REVERT: B 123 ILE cc_start: 0.9264 (mt) cc_final: 0.9007 (tt) REVERT: B 133 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 137 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8815 (mp0) REVERT: B 209 THR cc_start: 0.8801 (p) cc_final: 0.8525 (t) REVERT: B 288 ASP cc_start: 0.8262 (t0) cc_final: 0.7927 (p0) REVERT: B 289 ILE cc_start: 0.9131 (pt) cc_final: 0.8765 (tp) REVERT: B 297 ASN cc_start: 0.8664 (m-40) cc_final: 0.8425 (m110) REVERT: B 397 THR cc_start: 0.8859 (p) cc_final: 0.8610 (t) REVERT: B 430 HIS cc_start: 0.8737 (t-90) cc_final: 0.8429 (t70) REVERT: B 501 GLU cc_start: 0.8378 (mp0) cc_final: 0.7987 (mp0) REVERT: B 529 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8747 (tm-30) REVERT: B 572 MET cc_start: 0.8679 (tpp) cc_final: 0.8314 (tpp) REVERT: B 702 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 133 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: C 137 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8772 (mp0) REVERT: C 171 CYS cc_start: 0.8418 (t) cc_final: 0.8118 (t) REVERT: C 209 THR cc_start: 0.8756 (p) cc_final: 0.8508 (t) REVERT: C 288 ASP cc_start: 0.8434 (t0) cc_final: 0.7836 (p0) REVERT: C 289 ILE cc_start: 0.9107 (pt) cc_final: 0.8753 (tp) REVERT: C 291 SER cc_start: 0.8593 (t) cc_final: 0.8371 (p) REVERT: C 297 ASN cc_start: 0.8669 (m-40) cc_final: 0.8392 (m110) REVERT: C 501 GLU cc_start: 0.8382 (mp0) cc_final: 0.7987 (mp0) REVERT: C 529 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 555 MET cc_start: 0.7937 (mtp) cc_final: 0.7573 (ptp) REVERT: C 562 MET cc_start: 0.9129 (mmm) cc_final: 0.8911 (mmm) REVERT: C 572 MET cc_start: 0.8696 (tpp) cc_final: 0.8321 (tpp) REVERT: C 631 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7492 (tp30) REVERT: C 684 VAL cc_start: 0.8736 (t) cc_final: 0.8534 (p) REVERT: C 702 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 137 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8800 (mp0) REVERT: D 171 CYS cc_start: 0.8380 (t) cc_final: 0.8096 (t) REVERT: D 191 LEU cc_start: 0.9027 (mt) cc_final: 0.8259 (mt) REVERT: D 195 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7839 (mt-10) REVERT: D 209 THR cc_start: 0.8690 (p) cc_final: 0.8468 (t) REVERT: D 282 MET cc_start: 0.8082 (mtp) cc_final: 0.7738 (mmm) REVERT: D 288 ASP cc_start: 0.8360 (t0) cc_final: 0.7481 (p0) REVERT: D 289 ILE cc_start: 0.9080 (pt) cc_final: 0.8864 (tp) REVERT: D 293 ASP cc_start: 0.8186 (t0) cc_final: 0.7960 (t0) REVERT: D 297 ASN cc_start: 0.8591 (m-40) cc_final: 0.8292 (m110) REVERT: D 430 HIS cc_start: 0.8604 (t-90) cc_final: 0.8278 (t70) REVERT: D 446 CYS cc_start: 0.8588 (m) cc_final: 0.8146 (m) REVERT: D 501 GLU cc_start: 0.8424 (mp0) cc_final: 0.8086 (mp0) REVERT: D 529 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8524 (tm-30) REVERT: D 631 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7474 (tp30) outliers start: 108 outliers final: 24 residues processed: 673 average time/residue: 0.1404 time to fit residues: 150.0896 Evaluate side-chains 443 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 412 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 731 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 123 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 221 optimal weight: 0.0270 chunk 240 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 HIS A 750 ASN B 216 GLN B 645 GLN B 750 ASN C 430 HIS C 645 GLN C 750 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 750 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098070 restraints weight = 48494.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100613 restraints weight = 29856.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102338 restraints weight = 21439.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103503 restraints weight = 17225.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104171 restraints weight = 14840.042| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21476 Z= 0.149 Angle : 0.789 11.057 29036 Z= 0.395 Chirality : 0.043 0.181 3292 Planarity : 0.005 0.066 3616 Dihedral : 8.262 54.679 2844 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.50 % Favored : 88.03 % Rotamer: Outliers : 4.68 % Allowed : 15.76 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.16), residues: 2556 helix: -0.67 (0.13), residues: 1476 sheet: -1.67 (0.68), residues: 76 loop : -3.48 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 696 TYR 0.020 0.001 TYR A 451 PHE 0.024 0.002 PHE B 666 TRP 0.028 0.002 TRP B 710 HIS 0.005 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00315 (21472) covalent geometry : angle 0.78863 (29036) hydrogen bonds : bond 0.03892 ( 955) hydrogen bonds : angle 4.71063 ( 2805) Misc. bond : bond 0.00137 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 494 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: A 137 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8659 (pm20) REVERT: A 159 MET cc_start: 0.8186 (mmt) cc_final: 0.7902 (mmt) REVERT: A 209 THR cc_start: 0.8668 (p) cc_final: 0.8400 (t) REVERT: A 346 GLN cc_start: 0.8663 (mt0) cc_final: 0.8011 (mt0) REVERT: A 430 HIS cc_start: 0.8676 (t-90) cc_final: 0.8346 (t70) REVERT: A 446 CYS cc_start: 0.8577 (m) cc_final: 0.8175 (m) REVERT: A 479 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6554 (mpp) REVERT: A 529 GLN cc_start: 0.9095 (tm-30) cc_final: 0.8736 (tm-30) REVERT: A 596 LEU cc_start: 0.9036 (tt) cc_final: 0.8821 (tp) REVERT: A 631 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7638 (tm-30) REVERT: A 634 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8476 (mttm) REVERT: B 123 ILE cc_start: 0.9221 (mt) cc_final: 0.8983 (tt) REVERT: B 133 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7895 (mp0) REVERT: B 159 MET cc_start: 0.7951 (mmt) cc_final: 0.7565 (mmt) REVERT: B 209 THR cc_start: 0.8797 (p) cc_final: 0.8501 (t) REVERT: B 288 ASP cc_start: 0.8394 (t0) cc_final: 0.7859 (p0) REVERT: B 290 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8736 (p) REVERT: B 430 HIS cc_start: 0.8614 (t-90) cc_final: 0.8266 (t70) REVERT: B 479 MET cc_start: 0.5865 (mpp) cc_final: 0.5614 (mpp) REVERT: B 501 GLU cc_start: 0.8310 (mp0) cc_final: 0.8057 (mp0) REVERT: B 529 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8833 (tm-30) REVERT: B 572 MET cc_start: 0.8797 (tpp) cc_final: 0.8507 (tpp) REVERT: C 133 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 159 MET cc_start: 0.8150 (mmt) cc_final: 0.7888 (mmt) REVERT: C 171 CYS cc_start: 0.8429 (t) cc_final: 0.8130 (t) REVERT: C 193 PHE cc_start: 0.8572 (t80) cc_final: 0.8370 (t80) REVERT: C 209 THR cc_start: 0.8686 (p) cc_final: 0.8418 (t) REVERT: C 282 MET cc_start: 0.7879 (mmm) cc_final: 0.7575 (mmm) REVERT: C 288 ASP cc_start: 0.8484 (t0) cc_final: 0.7934 (p0) REVERT: C 290 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8652 (p) REVERT: C 291 SER cc_start: 0.8683 (t) cc_final: 0.8333 (p) REVERT: C 346 GLN cc_start: 0.8648 (mt0) cc_final: 0.8067 (mt0) REVERT: C 389 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 446 CYS cc_start: 0.8569 (m) cc_final: 0.8168 (m) REVERT: C 501 GLU cc_start: 0.8313 (mp0) cc_final: 0.7969 (mp0) REVERT: C 529 GLN cc_start: 0.8961 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 555 MET cc_start: 0.8102 (mtp) cc_final: 0.7895 (mtm) REVERT: C 572 MET cc_start: 0.8833 (tpp) cc_final: 0.8478 (tpp) REVERT: C 605 LEU cc_start: 0.8990 (tt) cc_final: 0.8535 (tt) REVERT: C 631 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7532 (tm-30) REVERT: D 117 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5758 (mttm) REVERT: D 137 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8666 (pm20) REVERT: D 159 MET cc_start: 0.8138 (mmt) cc_final: 0.7836 (mmt) REVERT: D 171 CYS cc_start: 0.8398 (t) cc_final: 0.8135 (t) REVERT: D 191 LEU cc_start: 0.9035 (mt) cc_final: 0.8340 (mt) REVERT: D 195 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7684 (mt-10) REVERT: D 209 THR cc_start: 0.8604 (p) cc_final: 0.8365 (t) REVERT: D 288 ASP cc_start: 0.8653 (t0) cc_final: 0.7715 (p0) REVERT: D 305 THR cc_start: 0.9229 (p) cc_final: 0.8970 (t) REVERT: D 346 GLN cc_start: 0.8607 (mt0) cc_final: 0.8019 (mt0) REVERT: D 389 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8438 (mt) REVERT: D 430 HIS cc_start: 0.8650 (t-90) cc_final: 0.8298 (t70) REVERT: D 446 CYS cc_start: 0.8589 (m) cc_final: 0.8157 (m) REVERT: D 479 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6512 (mpp) REVERT: D 529 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8597 (tm-30) REVERT: D 631 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7660 (tm-30) REVERT: D 702 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7621 (mm-30) outliers start: 107 outliers final: 48 residues processed: 563 average time/residue: 0.1459 time to fit residues: 129.9568 Evaluate side-chains 478 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 417 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 717 MET Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 717 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 645 GLN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 750 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 645 GLN ** D 750 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.114633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.093854 restraints weight = 49654.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096271 restraints weight = 30527.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097840 restraints weight = 21993.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.098965 restraints weight = 17792.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099588 restraints weight = 15358.572| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21476 Z= 0.200 Angle : 0.806 9.874 29036 Z= 0.406 Chirality : 0.044 0.187 3292 Planarity : 0.005 0.058 3616 Dihedral : 7.977 54.620 2842 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.36 % Favored : 87.17 % Rotamer: Outliers : 4.51 % Allowed : 18.74 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2556 helix: -0.36 (0.13), residues: 1496 sheet: -1.97 (0.65), residues: 76 loop : -3.38 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 371 TYR 0.021 0.002 TYR C 451 PHE 0.029 0.002 PHE B 666 TRP 0.018 0.002 TRP C 481 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00448 (21472) covalent geometry : angle 0.80608 (29036) hydrogen bonds : bond 0.03803 ( 955) hydrogen bonds : angle 4.59981 ( 2805) Misc. bond : bond 0.00056 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 420 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: A 159 MET cc_start: 0.8199 (mmt) cc_final: 0.7763 (mmt) REVERT: A 209 THR cc_start: 0.8672 (p) cc_final: 0.8442 (t) REVERT: A 293 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7404 (t0) REVERT: A 346 GLN cc_start: 0.8808 (mt0) cc_final: 0.8121 (mt0) REVERT: A 479 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6928 (mpp) REVERT: A 529 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 596 LEU cc_start: 0.9048 (tt) cc_final: 0.8818 (tp) REVERT: A 616 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7048 (pttm) REVERT: A 631 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7677 (tm-30) REVERT: A 634 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8373 (mttm) REVERT: A 720 LEU cc_start: 0.7976 (mm) cc_final: 0.7686 (mm) REVERT: A 732 LEU cc_start: 0.8573 (mt) cc_final: 0.8337 (mt) REVERT: B 159 MET cc_start: 0.8345 (mmt) cc_final: 0.8118 (mmt) REVERT: B 209 THR cc_start: 0.8767 (p) cc_final: 0.8515 (t) REVERT: B 216 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: B 257 GLU cc_start: 0.7037 (tt0) cc_final: 0.6706 (mt-10) REVERT: B 288 ASP cc_start: 0.8627 (t0) cc_final: 0.8023 (p0) REVERT: B 290 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 346 GLN cc_start: 0.8812 (mt0) cc_final: 0.8113 (mt0) REVERT: B 529 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8922 (tm-30) REVERT: B 555 MET cc_start: 0.8113 (mtm) cc_final: 0.7787 (ptp) REVERT: B 561 ASN cc_start: 0.8801 (m-40) cc_final: 0.8059 (t0) REVERT: B 562 MET cc_start: 0.9206 (mmp) cc_final: 0.8793 (mmm) REVERT: B 572 MET cc_start: 0.8910 (tpp) cc_final: 0.8671 (tpp) REVERT: B 722 LYS cc_start: 0.6769 (mttp) cc_final: 0.6534 (mttm) REVERT: C 133 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: C 159 MET cc_start: 0.8159 (mmt) cc_final: 0.7775 (mmt) REVERT: C 171 CYS cc_start: 0.8533 (t) cc_final: 0.8218 (t) REVERT: C 209 THR cc_start: 0.8686 (p) cc_final: 0.8437 (t) REVERT: C 282 MET cc_start: 0.7943 (mmm) cc_final: 0.7633 (mmm) REVERT: C 288 ASP cc_start: 0.8566 (t0) cc_final: 0.8064 (p0) REVERT: C 290 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8748 (p) REVERT: C 346 GLN cc_start: 0.8813 (mt0) cc_final: 0.8252 (mt0) REVERT: C 529 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 555 MET cc_start: 0.8275 (mtp) cc_final: 0.8022 (mtm) REVERT: C 572 MET cc_start: 0.9010 (tpp) cc_final: 0.8750 (tpp) REVERT: C 587 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8943 (p) REVERT: C 631 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7763 (tm-30) REVERT: C 632 LEU cc_start: 0.9329 (tt) cc_final: 0.9045 (tt) REVERT: C 722 LYS cc_start: 0.7091 (mttp) cc_final: 0.6796 (mttm) REVERT: C 732 LEU cc_start: 0.8209 (mt) cc_final: 0.7786 (mt) REVERT: D 159 MET cc_start: 0.8311 (mmt) cc_final: 0.7911 (mmt) REVERT: D 171 CYS cc_start: 0.8500 (t) cc_final: 0.8206 (t) REVERT: D 191 LEU cc_start: 0.9082 (mt) cc_final: 0.8799 (mt) REVERT: D 195 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 209 THR cc_start: 0.8590 (p) cc_final: 0.8384 (t) REVERT: D 276 GLU cc_start: 0.8420 (pm20) cc_final: 0.8211 (pm20) REVERT: D 288 ASP cc_start: 0.8489 (t0) cc_final: 0.7969 (p0) REVERT: D 290 THR cc_start: 0.8751 (m) cc_final: 0.8382 (p) REVERT: D 346 GLN cc_start: 0.8800 (mt0) cc_final: 0.8240 (mt0) REVERT: D 446 CYS cc_start: 0.8533 (m) cc_final: 0.8161 (m) REVERT: D 479 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6950 (mpp) REVERT: D 529 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8779 (tm-30) REVERT: D 610 GLU cc_start: 0.6942 (tp30) cc_final: 0.6651 (tp30) REVERT: D 616 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7132 (pttm) REVERT: D 631 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7826 (tm-30) REVERT: D 702 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7689 (mm-30) outliers start: 103 outliers final: 51 residues processed: 485 average time/residue: 0.1418 time to fit residues: 111.5922 Evaluate side-chains 444 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 381 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 742 TRP Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 137 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 227 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 750 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.113599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.092683 restraints weight = 49074.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095084 restraints weight = 30107.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096724 restraints weight = 21708.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097783 restraints weight = 17379.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098532 restraints weight = 14988.186| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21476 Z= 0.199 Angle : 0.798 12.427 29036 Z= 0.400 Chirality : 0.044 0.186 3292 Planarity : 0.004 0.054 3616 Dihedral : 7.648 59.568 2836 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.17 % Favored : 87.40 % Rotamer: Outliers : 4.47 % Allowed : 20.40 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2556 helix: -0.15 (0.13), residues: 1496 sheet: -2.36 (0.62), residues: 76 loop : -3.23 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 371 TYR 0.020 0.002 TYR C 451 PHE 0.024 0.002 PHE A 633 TRP 0.019 0.002 TRP C 481 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00445 (21472) covalent geometry : angle 0.79759 (29036) hydrogen bonds : bond 0.03702 ( 955) hydrogen bonds : angle 4.57648 ( 2805) Misc. bond : bond 0.00065 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 408 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8334 (mmt) cc_final: 0.7811 (mmt) REVERT: A 209 THR cc_start: 0.8719 (p) cc_final: 0.8508 (t) REVERT: A 288 ASP cc_start: 0.8791 (t0) cc_final: 0.7930 (p0) REVERT: A 293 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7501 (t0) REVERT: A 332 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 346 GLN cc_start: 0.8810 (mt0) cc_final: 0.8218 (mt0) REVERT: A 419 MET cc_start: 0.8603 (mtt) cc_final: 0.8253 (mtt) REVERT: A 529 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 561 ASN cc_start: 0.8825 (m-40) cc_final: 0.8406 (t0) REVERT: A 562 MET cc_start: 0.9042 (mmm) cc_final: 0.8364 (mmm) REVERT: A 596 LEU cc_start: 0.9038 (tt) cc_final: 0.8820 (tp) REVERT: A 616 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7034 (pttm) REVERT: A 634 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8395 (mttm) REVERT: B 141 ASP cc_start: 0.8497 (m-30) cc_final: 0.8257 (m-30) REVERT: B 159 MET cc_start: 0.8398 (mmt) cc_final: 0.8079 (mmt) REVERT: B 209 THR cc_start: 0.8797 (p) cc_final: 0.8549 (t) REVERT: B 288 ASP cc_start: 0.8644 (t0) cc_final: 0.8039 (p0) REVERT: B 290 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8644 (p) REVERT: B 346 GLN cc_start: 0.8783 (mt0) cc_final: 0.8121 (mt0) REVERT: B 419 MET cc_start: 0.8589 (mtt) cc_final: 0.8351 (mtt) REVERT: B 529 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8925 (tm-30) REVERT: B 561 ASN cc_start: 0.8819 (m-40) cc_final: 0.8414 (t0) REVERT: B 562 MET cc_start: 0.9153 (mmp) cc_final: 0.8853 (mmm) REVERT: B 572 MET cc_start: 0.9001 (tpp) cc_final: 0.8737 (tpp) REVERT: B 587 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8977 (p) REVERT: C 141 ASP cc_start: 0.8460 (m-30) cc_final: 0.8178 (m-30) REVERT: C 159 MET cc_start: 0.8272 (mmt) cc_final: 0.7853 (mmt) REVERT: C 171 CYS cc_start: 0.8580 (t) cc_final: 0.8296 (t) REVERT: C 288 ASP cc_start: 0.8676 (t0) cc_final: 0.8448 (t0) REVERT: C 290 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8766 (p) REVERT: C 291 SER cc_start: 0.9192 (t) cc_final: 0.8870 (p) REVERT: C 346 GLN cc_start: 0.8848 (mt0) cc_final: 0.8279 (mt0) REVERT: C 479 MET cc_start: 0.6781 (mpp) cc_final: 0.6085 (mpp) REVERT: C 529 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8760 (tm-30) REVERT: C 572 MET cc_start: 0.9087 (tpp) cc_final: 0.8824 (tpp) REVERT: C 598 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9254 (tp) REVERT: C 631 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7749 (tm-30) REVERT: D 159 MET cc_start: 0.8294 (mmt) cc_final: 0.7796 (mmt) REVERT: D 282 MET cc_start: 0.8066 (mmm) cc_final: 0.7857 (mmm) REVERT: D 288 ASP cc_start: 0.8517 (t0) cc_final: 0.7995 (p0) REVERT: D 290 THR cc_start: 0.8746 (m) cc_final: 0.8474 (p) REVERT: D 346 GLN cc_start: 0.8804 (mt0) cc_final: 0.8253 (mt0) REVERT: D 419 MET cc_start: 0.8579 (mtt) cc_final: 0.8286 (mtt) REVERT: D 529 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8748 (tm-30) REVERT: D 561 ASN cc_start: 0.8834 (m-40) cc_final: 0.8224 (t0) REVERT: D 610 GLU cc_start: 0.6942 (tp30) cc_final: 0.6689 (tp30) REVERT: D 616 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7114 (pttm) REVERT: D 631 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7827 (tm-30) REVERT: D 702 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7571 (mm-30) outliers start: 102 outliers final: 54 residues processed: 477 average time/residue: 0.1407 time to fit residues: 108.7439 Evaluate side-chains 415 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 353 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 742 TRP Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 110 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 HIS C 750 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093713 restraints weight = 48845.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096220 restraints weight = 29595.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097903 restraints weight = 21059.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099051 restraints weight = 16688.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099808 restraints weight = 14274.371| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21476 Z= 0.167 Angle : 0.779 11.961 29036 Z= 0.389 Chirality : 0.044 0.188 3292 Planarity : 0.004 0.050 3616 Dihedral : 7.508 60.238 2836 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.34 % Favored : 86.31 % Rotamer: Outliers : 3.98 % Allowed : 22.33 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2556 helix: -0.05 (0.13), residues: 1504 sheet: -2.56 (0.59), residues: 76 loop : -3.12 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.020 0.002 TYR C 451 PHE 0.031 0.002 PHE A 666 TRP 0.023 0.002 TRP C 710 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00378 (21472) covalent geometry : angle 0.77898 (29036) hydrogen bonds : bond 0.03569 ( 955) hydrogen bonds : angle 4.53742 ( 2805) Misc. bond : bond 0.00066 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 390 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8324 (mmt) cc_final: 0.7774 (mmt) REVERT: A 209 THR cc_start: 0.8706 (p) cc_final: 0.8504 (t) REVERT: A 293 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7607 (t0) REVERT: A 419 MET cc_start: 0.8689 (mtt) cc_final: 0.8331 (mtt) REVERT: A 479 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6371 (mpp) REVERT: A 529 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 561 ASN cc_start: 0.8827 (m-40) cc_final: 0.8444 (t0) REVERT: A 562 MET cc_start: 0.9045 (mmm) cc_final: 0.8049 (mmm) REVERT: A 596 LEU cc_start: 0.9036 (tt) cc_final: 0.8793 (tp) REVERT: A 616 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7123 (pttm) REVERT: A 702 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 159 MET cc_start: 0.8364 (mmt) cc_final: 0.8064 (mmt) REVERT: B 288 ASP cc_start: 0.8691 (t0) cc_final: 0.8017 (p0) REVERT: B 290 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 346 GLN cc_start: 0.8849 (mt0) cc_final: 0.8226 (mt0) REVERT: B 419 MET cc_start: 0.8656 (mtt) cc_final: 0.8359 (mtt) REVERT: B 479 MET cc_start: 0.6369 (mpp) cc_final: 0.5958 (mpp) REVERT: B 529 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8901 (tm-30) REVERT: B 561 ASN cc_start: 0.8767 (m-40) cc_final: 0.8379 (t0) REVERT: B 562 MET cc_start: 0.9074 (mmp) cc_final: 0.8858 (mmm) REVERT: B 572 MET cc_start: 0.9035 (tpp) cc_final: 0.8815 (tpp) REVERT: B 574 MET cc_start: 0.9096 (mmp) cc_final: 0.8889 (mmt) REVERT: B 587 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8927 (p) REVERT: B 702 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7703 (mm-30) REVERT: B 748 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: C 137 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8713 (pm20) REVERT: C 159 MET cc_start: 0.8313 (mmt) cc_final: 0.7816 (mmt) REVERT: C 171 CYS cc_start: 0.8555 (t) cc_final: 0.8246 (t) REVERT: C 276 GLU cc_start: 0.8595 (pm20) cc_final: 0.8340 (pm20) REVERT: C 282 MET cc_start: 0.7883 (mmm) cc_final: 0.7618 (mmm) REVERT: C 290 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 291 SER cc_start: 0.9083 (t) cc_final: 0.8733 (p) REVERT: C 346 GLN cc_start: 0.8748 (mt0) cc_final: 0.8219 (mp10) REVERT: C 446 CYS cc_start: 0.8598 (m) cc_final: 0.8108 (m) REVERT: C 479 MET cc_start: 0.6634 (mpp) cc_final: 0.5986 (mpp) REVERT: C 529 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8720 (tm-30) REVERT: C 555 MET cc_start: 0.8342 (mtp) cc_final: 0.8073 (mtm) REVERT: C 572 MET cc_start: 0.9101 (tpp) cc_final: 0.8813 (tpp) REVERT: C 574 MET cc_start: 0.9035 (mmp) cc_final: 0.8780 (mmt) REVERT: C 598 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9183 (tp) REVERT: C 631 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7782 (tm-30) REVERT: C 722 LYS cc_start: 0.6561 (mtpp) cc_final: 0.6253 (mttm) REVERT: D 159 MET cc_start: 0.8313 (mmt) cc_final: 0.7773 (mmt) REVERT: D 288 ASP cc_start: 0.8547 (t0) cc_final: 0.7989 (p0) REVERT: D 290 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (p) REVERT: D 419 MET cc_start: 0.8677 (mtt) cc_final: 0.8365 (mtt) REVERT: D 479 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6331 (mpp) REVERT: D 529 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8747 (tm-30) REVERT: D 561 ASN cc_start: 0.8862 (m-40) cc_final: 0.8152 (t0) REVERT: D 574 MET cc_start: 0.9113 (tpp) cc_final: 0.8850 (mmp) REVERT: D 610 GLU cc_start: 0.6846 (tp30) cc_final: 0.6593 (tp30) REVERT: D 616 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7247 (pttm) outliers start: 91 outliers final: 56 residues processed: 451 average time/residue: 0.1409 time to fit residues: 102.2414 Evaluate side-chains 424 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 356 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 742 TRP Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 159 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094814 restraints weight = 48713.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097308 restraints weight = 29651.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099010 restraints weight = 21098.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100131 restraints weight = 16756.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100784 restraints weight = 14353.335| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21476 Z= 0.146 Angle : 0.786 15.075 29036 Z= 0.388 Chirality : 0.043 0.299 3292 Planarity : 0.004 0.078 3616 Dihedral : 7.335 60.762 2836 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.64 % Favored : 87.05 % Rotamer: Outliers : 3.55 % Allowed : 23.51 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.17), residues: 2556 helix: 0.22 (0.13), residues: 1472 sheet: -2.74 (0.57), residues: 72 loop : -2.81 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.020 0.002 TYR C 451 PHE 0.030 0.001 PHE B 666 TRP 0.024 0.002 TRP B 710 HIS 0.003 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00333 (21472) covalent geometry : angle 0.78574 (29036) hydrogen bonds : bond 0.03430 ( 955) hydrogen bonds : angle 4.48663 ( 2805) Misc. bond : bond 0.00065 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 410 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8285 (mmt) cc_final: 0.7771 (mmt) REVERT: A 293 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7511 (t0) REVERT: A 419 MET cc_start: 0.8589 (mtt) cc_final: 0.8377 (mtt) REVERT: A 446 CYS cc_start: 0.8522 (m) cc_final: 0.8053 (m) REVERT: A 479 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6250 (mpp) REVERT: A 529 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 561 ASN cc_start: 0.8770 (m-40) cc_final: 0.8400 (t0) REVERT: A 562 MET cc_start: 0.9029 (mmm) cc_final: 0.8086 (mmm) REVERT: A 596 LEU cc_start: 0.9040 (tt) cc_final: 0.8809 (tp) REVERT: A 616 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7373 (tptp) REVERT: B 159 MET cc_start: 0.8393 (mmt) cc_final: 0.8081 (mmt) REVERT: B 288 ASP cc_start: 0.8757 (t0) cc_final: 0.7896 (p0) REVERT: B 290 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 346 GLN cc_start: 0.8807 (mt0) cc_final: 0.8180 (mt0) REVERT: B 392 LEU cc_start: 0.8612 (tp) cc_final: 0.8330 (tt) REVERT: B 419 MET cc_start: 0.8678 (mtt) cc_final: 0.8404 (mtt) REVERT: B 529 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8862 (tm-30) REVERT: B 555 MET cc_start: 0.8332 (ptp) cc_final: 0.8074 (ptp) REVERT: B 561 ASN cc_start: 0.8717 (m-40) cc_final: 0.8327 (t0) REVERT: B 572 MET cc_start: 0.9024 (tpp) cc_final: 0.8824 (tpp) REVERT: B 574 MET cc_start: 0.9158 (mmp) cc_final: 0.8782 (mmt) REVERT: B 748 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: C 137 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: C 141 ASP cc_start: 0.8432 (m-30) cc_final: 0.8154 (m-30) REVERT: C 159 MET cc_start: 0.8265 (mmt) cc_final: 0.7772 (mmt) REVERT: C 171 CYS cc_start: 0.8461 (t) cc_final: 0.8152 (t) REVERT: C 282 MET cc_start: 0.7886 (mmm) cc_final: 0.7568 (mmm) REVERT: C 288 ASP cc_start: 0.8327 (t0) cc_final: 0.7941 (p0) REVERT: C 346 GLN cc_start: 0.8765 (mt0) cc_final: 0.8098 (mp10) REVERT: C 479 MET cc_start: 0.6468 (mpp) cc_final: 0.5999 (mpp) REVERT: C 529 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8760 (tm-30) REVERT: C 555 MET cc_start: 0.8312 (mtp) cc_final: 0.8056 (mtm) REVERT: C 572 MET cc_start: 0.9065 (tpp) cc_final: 0.8808 (tpp) REVERT: C 574 MET cc_start: 0.9162 (mmp) cc_final: 0.8686 (mmt) REVERT: C 598 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9152 (tp) REVERT: D 159 MET cc_start: 0.8318 (mmt) cc_final: 0.7709 (mmt) REVERT: D 282 MET cc_start: 0.8019 (mmm) cc_final: 0.7655 (mmm) REVERT: D 288 ASP cc_start: 0.8574 (t0) cc_final: 0.7939 (p0) REVERT: D 290 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8449 (p) REVERT: D 346 GLN cc_start: 0.8741 (mt0) cc_final: 0.8126 (mt0) REVERT: D 419 MET cc_start: 0.8600 (mtt) cc_final: 0.8333 (mtt) REVERT: D 479 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6245 (mpp) REVERT: D 529 GLN cc_start: 0.9188 (tm-30) cc_final: 0.8765 (tm-30) REVERT: D 561 ASN cc_start: 0.8773 (m-40) cc_final: 0.8123 (t0) REVERT: D 574 MET cc_start: 0.9019 (tpp) cc_final: 0.8734 (mmp) REVERT: D 598 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9123 (tp) REVERT: D 610 GLU cc_start: 0.6829 (tp30) cc_final: 0.6567 (tp30) REVERT: D 669 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8571 (tm) outliers start: 81 outliers final: 50 residues processed: 458 average time/residue: 0.1398 time to fit residues: 103.3569 Evaluate side-chains 430 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 369 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 742 TRP Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 742 TRP Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 742 TRP Chi-restraints excluded: chain D residue 748 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 192 optimal weight: 20.0000 chunk 113 optimal weight: 0.2980 chunk 188 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 212 optimal weight: 0.1980 chunk 220 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 ASN C 297 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.118746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097648 restraints weight = 48813.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100053 restraints weight = 30598.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101716 restraints weight = 22298.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102816 restraints weight = 17919.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103556 restraints weight = 15517.742| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21476 Z= 0.136 Angle : 0.803 15.027 29036 Z= 0.391 Chirality : 0.043 0.304 3292 Planarity : 0.004 0.055 3616 Dihedral : 7.146 59.848 2836 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.79 % Favored : 86.93 % Rotamer: Outliers : 3.68 % Allowed : 23.91 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2556 helix: 0.35 (0.14), residues: 1460 sheet: -3.09 (0.53), residues: 76 loop : -2.69 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 733 TYR 0.024 0.001 TYR D 661 PHE 0.027 0.001 PHE C 666 TRP 0.018 0.001 TRP B 481 HIS 0.002 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00307 (21472) covalent geometry : angle 0.80268 (29036) hydrogen bonds : bond 0.03334 ( 955) hydrogen bonds : angle 4.48082 ( 2805) Misc. bond : bond 0.00066 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 419 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8233 (mmt) cc_final: 0.7718 (mmt) REVERT: A 171 CYS cc_start: 0.8757 (t) cc_final: 0.8249 (t) REVERT: A 293 ASP cc_start: 0.7783 (OUTLIER) cc_final: 0.7336 (t0) REVERT: A 419 MET cc_start: 0.8552 (mtt) cc_final: 0.8332 (mtt) REVERT: A 446 CYS cc_start: 0.8391 (m) cc_final: 0.7892 (m) REVERT: A 479 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6190 (mpp) REVERT: A 529 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 555 MET cc_start: 0.7973 (ptp) cc_final: 0.7703 (ptp) REVERT: A 561 ASN cc_start: 0.8615 (m-40) cc_final: 0.8382 (t0) REVERT: A 562 MET cc_start: 0.8932 (mmm) cc_final: 0.7993 (mmm) REVERT: A 596 LEU cc_start: 0.9057 (tt) cc_final: 0.8835 (tp) REVERT: A 616 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7462 (tptt) REVERT: A 634 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8239 (mttm) REVERT: A 656 PHE cc_start: 0.8525 (m-10) cc_final: 0.8312 (m-80) REVERT: A 710 TRP cc_start: 0.6790 (OUTLIER) cc_final: 0.6518 (p-90) REVERT: B 159 MET cc_start: 0.8335 (mmt) cc_final: 0.7981 (mmt) REVERT: B 171 CYS cc_start: 0.8742 (t) cc_final: 0.8238 (t) REVERT: B 288 ASP cc_start: 0.8702 (t0) cc_final: 0.7761 (p0) REVERT: B 290 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8627 (p) REVERT: B 370 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (pp) REVERT: B 371 ARG cc_start: 0.7601 (tmm160) cc_final: 0.7392 (tmm160) REVERT: B 419 MET cc_start: 0.8566 (mtt) cc_final: 0.8304 (mtt) REVERT: B 446 CYS cc_start: 0.8551 (m) cc_final: 0.8079 (m) REVERT: B 479 MET cc_start: 0.6447 (mpp) cc_final: 0.6064 (mpp) REVERT: B 529 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8767 (tm-30) REVERT: B 555 MET cc_start: 0.8305 (ptp) cc_final: 0.8101 (ptp) REVERT: B 561 ASN cc_start: 0.8666 (m-40) cc_final: 0.8421 (t0) REVERT: B 574 MET cc_start: 0.9100 (mmp) cc_final: 0.8677 (mmt) REVERT: B 611 LYS cc_start: 0.3564 (tmtt) cc_final: 0.3242 (tmtt) REVERT: B 702 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 748 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: C 137 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: C 159 MET cc_start: 0.8203 (mmt) cc_final: 0.7680 (mmt) REVERT: C 171 CYS cc_start: 0.8361 (t) cc_final: 0.8077 (t) REVERT: C 288 ASP cc_start: 0.8201 (t0) cc_final: 0.7720 (p0) REVERT: C 346 GLN cc_start: 0.8678 (mt0) cc_final: 0.8118 (mt0) REVERT: C 479 MET cc_start: 0.6521 (mpp) cc_final: 0.6074 (mpp) REVERT: C 529 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8692 (tm-30) REVERT: C 555 MET cc_start: 0.8272 (mtp) cc_final: 0.7930 (mtm) REVERT: C 562 MET cc_start: 0.8886 (mmm) cc_final: 0.8388 (mmm) REVERT: C 574 MET cc_start: 0.9054 (mmp) cc_final: 0.8799 (mmt) REVERT: C 598 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9070 (tp) REVERT: C 702 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7634 (mm-30) REVERT: C 748 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6303 (m-80) REVERT: D 159 MET cc_start: 0.8221 (mmt) cc_final: 0.7700 (mmt) REVERT: D 290 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8153 (p) REVERT: D 419 MET cc_start: 0.8492 (mtt) cc_final: 0.8262 (mtt) REVERT: D 479 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6184 (mpp) REVERT: D 529 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8865 (tm-30) REVERT: D 561 ASN cc_start: 0.8724 (m-40) cc_final: 0.8191 (t0) REVERT: D 610 GLU cc_start: 0.6686 (tp30) cc_final: 0.6446 (tp30) REVERT: D 677 MET cc_start: 0.7355 (mmm) cc_final: 0.7152 (tpp) REVERT: D 702 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7631 (mm-30) outliers start: 84 outliers final: 41 residues processed: 468 average time/residue: 0.1381 time to fit residues: 104.1799 Evaluate side-chains 415 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 710 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 99 optimal weight: 0.0010 chunk 229 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096602 restraints weight = 48846.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099070 restraints weight = 29956.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100762 restraints weight = 21414.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101871 restraints weight = 17068.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102493 restraints weight = 14670.798| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 21476 Z= 0.150 Angle : 0.813 13.457 29036 Z= 0.397 Chirality : 0.044 0.287 3292 Planarity : 0.004 0.046 3616 Dihedral : 7.124 63.207 2836 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.52 % Favored : 87.17 % Rotamer: Outliers : 3.06 % Allowed : 25.61 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2556 helix: 0.33 (0.14), residues: 1472 sheet: -3.08 (0.55), residues: 72 loop : -2.71 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 733 TYR 0.025 0.002 TYR C 661 PHE 0.037 0.001 PHE C 666 TRP 0.024 0.002 TRP A 481 HIS 0.002 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00344 (21472) covalent geometry : angle 0.81309 (29036) hydrogen bonds : bond 0.03395 ( 955) hydrogen bonds : angle 4.49828 ( 2805) Misc. bond : bond 0.00046 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 373 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8340 (mmt) cc_final: 0.7869 (mmt) REVERT: A 293 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7249 (t0) REVERT: A 419 MET cc_start: 0.8612 (mtt) cc_final: 0.8360 (mtt) REVERT: A 446 CYS cc_start: 0.8394 (m) cc_final: 0.7878 (m) REVERT: A 479 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5885 (mpp) REVERT: A 529 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8762 (tm-30) REVERT: A 562 MET cc_start: 0.9021 (mmm) cc_final: 0.8350 (mmm) REVERT: A 596 LEU cc_start: 0.9082 (tt) cc_final: 0.8839 (tp) REVERT: A 616 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7385 (tptt) REVERT: A 634 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8171 (mttm) REVERT: A 710 TRP cc_start: 0.6818 (OUTLIER) cc_final: 0.6531 (p-90) REVERT: B 159 MET cc_start: 0.8361 (mmt) cc_final: 0.8021 (mmt) REVERT: B 290 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 370 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8163 (pp) REVERT: B 419 MET cc_start: 0.8625 (mtt) cc_final: 0.8308 (mtt) REVERT: B 446 CYS cc_start: 0.8573 (m) cc_final: 0.8073 (m) REVERT: B 561 ASN cc_start: 0.8742 (m-40) cc_final: 0.8229 (t0) REVERT: B 574 MET cc_start: 0.9140 (mmp) cc_final: 0.8819 (mmt) REVERT: B 657 LEU cc_start: 0.9006 (tt) cc_final: 0.8792 (tp) REVERT: B 702 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 748 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6114 (m-80) REVERT: C 159 MET cc_start: 0.8207 (mmt) cc_final: 0.7698 (mmt) REVERT: C 171 CYS cc_start: 0.8414 (t) cc_final: 0.8112 (t) REVERT: C 288 ASP cc_start: 0.8436 (t0) cc_final: 0.7846 (p0) REVERT: C 346 GLN cc_start: 0.8758 (mt0) cc_final: 0.8164 (mt0) REVERT: C 479 MET cc_start: 0.6547 (mpp) cc_final: 0.6169 (mpp) REVERT: C 529 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 562 MET cc_start: 0.8952 (mmm) cc_final: 0.8422 (mmm) REVERT: C 574 MET cc_start: 0.9114 (mmp) cc_final: 0.8726 (mmt) REVERT: C 598 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9022 (tp) REVERT: C 748 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: D 159 MET cc_start: 0.8269 (mmt) cc_final: 0.7904 (mmt) REVERT: D 288 ASP cc_start: 0.8424 (t0) cc_final: 0.7893 (p0) REVERT: D 346 GLN cc_start: 0.8755 (mt0) cc_final: 0.8121 (mt0) REVERT: D 419 MET cc_start: 0.8517 (mtt) cc_final: 0.8298 (mtt) REVERT: D 479 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5957 (mpp) REVERT: D 529 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 574 MET cc_start: 0.8984 (mmp) cc_final: 0.8710 (mmt) REVERT: D 598 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9097 (tp) REVERT: D 610 GLU cc_start: 0.6752 (tp30) cc_final: 0.6485 (tp30) REVERT: D 657 LEU cc_start: 0.9136 (tt) cc_final: 0.8909 (tp) outliers start: 70 outliers final: 43 residues processed: 416 average time/residue: 0.1392 time to fit residues: 94.0277 Evaluate side-chains 410 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 355 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095667 restraints weight = 49029.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098120 restraints weight = 30275.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099789 restraints weight = 21810.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100902 restraints weight = 17485.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101562 restraints weight = 15064.704| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21476 Z= 0.160 Angle : 0.827 13.783 29036 Z= 0.405 Chirality : 0.044 0.266 3292 Planarity : 0.004 0.047 3616 Dihedral : 7.206 64.936 2836 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.95 % Favored : 86.74 % Rotamer: Outliers : 2.89 % Allowed : 25.74 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.17), residues: 2556 helix: 0.31 (0.13), residues: 1468 sheet: -3.07 (0.55), residues: 72 loop : -2.65 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 733 TYR 0.025 0.002 TYR A 661 PHE 0.033 0.002 PHE C 666 TRP 0.027 0.002 TRP A 742 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00366 (21472) covalent geometry : angle 0.82689 (29036) hydrogen bonds : bond 0.03408 ( 955) hydrogen bonds : angle 4.55162 ( 2805) Misc. bond : bond 0.00048 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5112 Ramachandran restraints generated. 2556 Oldfield, 0 Emsley, 2556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 373 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.8347 (mmt) cc_final: 0.7875 (mmt) REVERT: A 293 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7137 (t0) REVERT: A 346 GLN cc_start: 0.8782 (mt0) cc_final: 0.8119 (mt0) REVERT: A 419 MET cc_start: 0.8607 (mtt) cc_final: 0.8296 (mtt) REVERT: A 446 CYS cc_start: 0.8404 (m) cc_final: 0.7877 (m) REVERT: A 479 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.5821 (mpp) REVERT: A 529 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8736 (tm-30) REVERT: A 561 ASN cc_start: 0.8656 (t0) cc_final: 0.8269 (t0) REVERT: A 562 MET cc_start: 0.9039 (mmm) cc_final: 0.8514 (tpp) REVERT: A 596 LEU cc_start: 0.9094 (tt) cc_final: 0.8866 (tp) REVERT: A 616 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7435 (tptt) REVERT: A 634 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8156 (mttm) REVERT: B 159 MET cc_start: 0.8379 (mmt) cc_final: 0.8013 (mmt) REVERT: B 257 GLU cc_start: 0.5862 (mm-30) cc_final: 0.5629 (mm-30) REVERT: B 290 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 370 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8293 (pp) REVERT: B 419 MET cc_start: 0.8628 (mtt) cc_final: 0.8238 (mtt) REVERT: B 538 PHE cc_start: 0.8147 (m-80) cc_final: 0.7943 (m-10) REVERT: B 561 ASN cc_start: 0.8701 (m-40) cc_final: 0.8470 (t0) REVERT: B 574 MET cc_start: 0.9172 (mmp) cc_final: 0.8869 (mmt) REVERT: B 657 LEU cc_start: 0.9081 (tt) cc_final: 0.8844 (tp) REVERT: B 702 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 748 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6020 (m-80) REVERT: C 159 MET cc_start: 0.8265 (mmt) cc_final: 0.7823 (mmt) REVERT: C 171 CYS cc_start: 0.8446 (t) cc_final: 0.8136 (t) REVERT: C 288 ASP cc_start: 0.8426 (t0) cc_final: 0.7817 (p0) REVERT: C 346 GLN cc_start: 0.8811 (mt0) cc_final: 0.8192 (mt0) REVERT: C 479 MET cc_start: 0.6739 (mpp) cc_final: 0.6203 (mpp) REVERT: C 529 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8736 (tm-30) REVERT: C 561 ASN cc_start: 0.8725 (t0) cc_final: 0.8127 (t0) REVERT: C 562 MET cc_start: 0.9006 (mmm) cc_final: 0.8433 (mmm) REVERT: C 574 MET cc_start: 0.9136 (mmp) cc_final: 0.8807 (mmt) REVERT: C 598 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9056 (tp) REVERT: C 657 LEU cc_start: 0.9061 (tt) cc_final: 0.8824 (tp) REVERT: C 748 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: D 159 MET cc_start: 0.8295 (mmt) cc_final: 0.7995 (mmt) REVERT: D 288 ASP cc_start: 0.8454 (t0) cc_final: 0.7887 (p0) REVERT: D 346 GLN cc_start: 0.8803 (mt0) cc_final: 0.8072 (mt0) REVERT: D 419 MET cc_start: 0.8526 (mtt) cc_final: 0.8303 (mtt) REVERT: D 479 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5700 (mpp) REVERT: D 529 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8694 (tm-30) REVERT: D 561 ASN cc_start: 0.8644 (t0) cc_final: 0.7968 (t0) REVERT: D 562 MET cc_start: 0.8997 (mmm) cc_final: 0.8306 (mmm) REVERT: D 574 MET cc_start: 0.9124 (mmp) cc_final: 0.8874 (mmt) REVERT: D 598 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9131 (tp) REVERT: D 610 GLU cc_start: 0.6752 (tp30) cc_final: 0.6478 (tp30) REVERT: D 657 LEU cc_start: 0.9061 (tt) cc_final: 0.8857 (tp) outliers start: 66 outliers final: 48 residues processed: 416 average time/residue: 0.1371 time to fit residues: 92.5032 Evaluate side-chains 417 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 358 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 263 GLU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 704 GLU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 710 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 125 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 216 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 223 optimal weight: 0.0060 chunk 177 optimal weight: 0.4980 chunk 140 optimal weight: 4.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS B 750 ASN C 471 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 750 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.121539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100584 restraints weight = 48674.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103014 restraints weight = 30419.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104658 restraints weight = 22058.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105771 restraints weight = 17774.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106404 restraints weight = 15345.193| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21476 Z= 0.135 Angle : 0.830 15.755 29036 Z= 0.398 Chirality : 0.043 0.268 3292 Planarity : 0.004 0.046 3616 Dihedral : 7.054 65.021 2836 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.58 % Favored : 88.15 % Rotamer: Outliers : 2.32 % Allowed : 26.40 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.17), residues: 2556 helix: 0.38 (0.14), residues: 1480 sheet: -2.96 (0.55), residues: 72 loop : -2.66 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 337 TYR 0.021 0.001 TYR C 451 PHE 0.033 0.001 PHE A 193 TRP 0.021 0.001 TRP A 481 HIS 0.002 0.000 HIS B 471 Details of bonding type rmsd covalent geometry : bond 0.00299 (21472) covalent geometry : angle 0.83015 (29036) hydrogen bonds : bond 0.03281 ( 955) hydrogen bonds : angle 4.50742 ( 2805) Misc. bond : bond 0.00057 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.24 seconds wall clock time: 62 minutes 26.17 seconds (3746.17 seconds total)