Starting phenix.real_space_refine on Sun Sep 13 04:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.cif" model { file = "/net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dvy_8920/09_2026/6dvy_8920.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.26, per 1000 atoms: 0.30 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: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.53 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: 3.30 Time building geometry restraints manager: 2.32 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: 12268 22.22 - 44.45: 472 44.45 - 66.67: 20 66.67 - 88.90: 28 88.90 - 111.12: 8 Dihedral angle restraints: 12796 sinusoidal: 5228 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 12793 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: 0.07 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: 0.010 Normalize map: mean=0, sd=1: 0.600 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.430 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 12.525 111.121 7884 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/Z covalent geometry : bond 0.00803 / 0.37 (21472) covalent geometry : angle 1.25197 / 0.71 (29036) hydrogen bonds : bond 0.30247 / 19.52 ( 955) hydrogen bonds : angle 10.28743 / 7.07 ( 2805) Misc. bond : bond 0.29462 / 14.78 ( 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 : 0.815 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: 0.9164 (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: 0.8592 (tt) REVERT: A 288 ASP cc_start: 0.8453 (t0) cc_final: 0.7530 (p0) REVERT: A 291 SER cc_start: 0.8611 (t) cc_final: 0.8347 (p) REVERT: A 293 ASP cc_start: 0.8417 (t0) cc_final: 0.7926 (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: 0.7758 (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: 0.8976 (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: 0.8361 (m-40) cc_final: 0.7870 (m-40) REVERT: A 688 SER cc_start: 0.9427 (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: 0.8631 (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: 0.8461 (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: 0.7486 (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: 0.8825 (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: 0.8807 (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: 0.8830 (p) REVERT: D 171 CYS cc_start: 0.8478 (t) cc_final: 0.8143 (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: 0.7457 (t0) REVERT: D 373 LEU cc_start: 0.8836 (mt) cc_final: 0.8071 (mt) REVERT: D 444 SER cc_start: 0.9164 (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: 0.9025 (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: 0.1486 time to fit residues: 197.0164 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 : 0.801 ------------------------------------------------------------------------------- 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... 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 = 0.3639 r_free = 0.3639 target = 0.119492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098817 restraints weight = 48285.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101475 restraints weight = 28681.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103264 restraints weight = 20190.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104458 restraints weight = 15997.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105160 restraints weight = 13670.097| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21476 Z= 0.161 Angle : 0.875 13.777 29036 Z= 0.438 Chirality : 0.044 0.193 3292 Planarity : 0.006 0.072 3616 Dihedral : 9.102 79.907 2828 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.97 % Favored : 87.56 % Rotamer: Outliers : 4.64 % Allowed : 12.78 % Favored : 82.57 % 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: -3.72 (0.14), residues: 2556 helix: -1.79 (0.11), residues: 1464 sheet: -1.39 (0.68), residues: 76 loop : -3.54 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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/Z covalent geometry : bond 0.00349 / 0.16 (21472) covalent geometry : angle 0.87516 / 0.44 (29036) hydrogen bonds : bond 0.04930 / 3.25 ( 955) hydrogen bonds : angle 5.24892 / 3.58 ( 2805) Misc. bond : bond 0.00108 / 0.05 ( 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 700 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 594 time to evaluate : 0.756 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: 0.8327 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: A 137 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8687 (pm20) REVERT: A 171 CYS cc_start: 0.8470 (t) cc_final: 0.8171 (t) REVERT: A 191 LEU cc_start: 0.9080 (mt) cc_final: 0.8350 (mt) REVERT: A 195 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 209 THR cc_start: 0.8749 (p) cc_final: 0.8503 (t) REVERT: A 282 MET cc_start: 0.8254 (mtp) cc_final: 0.7878 (mmm) REVERT: A 336 MET cc_start: 0.8732 (ttm) cc_final: 0.8487 (ttm) REVERT: A 346 GLN cc_start: 0.8718 (mt0) cc_final: 0.8124 (mt0) REVERT: A 430 HIS cc_start: 0.8639 (t-90) cc_final: 0.8301 (t70) REVERT: A 446 CYS cc_start: 0.8652 (m) cc_final: 0.8221 (m) REVERT: A 501 GLU cc_start: 0.8459 (mp0) cc_final: 0.8089 (mp0) REVERT: A 529 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 631 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7372 (tp30) REVERT: A 702 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 710 TRP cc_start: 0.7484 (p-90) cc_final: 0.7274 (p-90) REVERT: B 123 ILE cc_start: 0.9284 (mt) cc_final: 0.9027 (tt) REVERT: B 129 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8344 (tm-30) REVERT: B 133 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: B 137 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8720 (pm20) REVERT: B 209 THR cc_start: 0.8808 (p) cc_final: 0.8535 (t) REVERT: B 282 MET cc_start: 0.8026 (mtp) cc_final: 0.7811 (mmm) REVERT: B 288 ASP cc_start: 0.8285 (t0) cc_final: 0.7926 (p0) REVERT: B 289 ILE cc_start: 0.9143 (pt) cc_final: 0.8750 (tp) REVERT: B 297 ASN cc_start: 0.8716 (m-40) cc_final: 0.8442 (m110) REVERT: B 397 THR cc_start: 0.8878 (p) cc_final: 0.8638 (t) REVERT: B 430 HIS cc_start: 0.8643 (t-90) cc_final: 0.8358 (t70) REVERT: B 501 GLU cc_start: 0.8427 (mp0) cc_final: 0.8082 (mp0) REVERT: B 529 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8761 (tm-30) REVERT: B 572 MET cc_start: 0.8720 (tpp) cc_final: 0.8390 (tpp) REVERT: B 702 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7738 (mm-30) REVERT: C 133 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: C 137 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: C 171 CYS cc_start: 0.8461 (t) cc_final: 0.8171 (t) REVERT: C 209 THR cc_start: 0.8764 (p) cc_final: 0.8521 (t) REVERT: C 288 ASP cc_start: 0.8455 (t0) cc_final: 0.7840 (p0) REVERT: C 289 ILE cc_start: 0.9117 (pt) cc_final: 0.8742 (tp) REVERT: C 291 SER cc_start: 0.8595 (t) cc_final: 0.8364 (p) REVERT: C 297 ASN cc_start: 0.8719 (m-40) cc_final: 0.8416 (m110) REVERT: C 501 GLU cc_start: 0.8431 (mp0) cc_final: 0.8209 (mp0) REVERT: C 529 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8602 (tm-30) REVERT: C 555 MET cc_start: 0.7807 (mtp) cc_final: 0.7463 (ptp) REVERT: C 562 MET cc_start: 0.9151 (mmm) cc_final: 0.8885 (mmm) REVERT: C 572 MET cc_start: 0.8724 (tpp) cc_final: 0.8364 (tpp) REVERT: C 631 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7492 (tp30) REVERT: C 684 VAL cc_start: 0.8752 (t) cc_final: 0.8547 (p) REVERT: C 702 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7665 (mm-30) REVERT: D 137 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8787 (mp0) REVERT: D 171 CYS cc_start: 0.8416 (t) cc_final: 0.8131 (t) REVERT: D 191 LEU cc_start: 0.9077 (mt) cc_final: 0.8391 (mt) REVERT: D 195 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 209 THR cc_start: 0.8698 (p) cc_final: 0.8475 (t) REVERT: D 282 MET cc_start: 0.8147 (mtp) cc_final: 0.7773 (mmm) REVERT: D 288 ASP cc_start: 0.8382 (t0) cc_final: 0.7476 (p0) REVERT: D 291 SER cc_start: 0.8522 (t) cc_final: 0.8305 (p) REVERT: D 297 ASN cc_start: 0.8651 (m-40) cc_final: 0.8367 (m110) REVERT: D 430 HIS cc_start: 0.8644 (t-90) cc_final: 0.8286 (t70) REVERT: D 446 CYS cc_start: 0.8611 (m) cc_final: 0.8148 (m) REVERT: D 501 GLU cc_start: 0.8473 (mp0) cc_final: 0.8119 (mp0) REVERT: D 529 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 631 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7484 (tp30) outliers start: 106 outliers final: 21 residues processed: 666 average time/residue: 0.1409 time to fit residues: 149.9209 Evaluate side-chains 447 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 419 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 B residue 133 GLU 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 137 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 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: 9.9990 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 198 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 28 optimal weight: 0.0470 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 HIS B 216 GLN B 227 GLN B 645 GLN C 227 GLN C 645 GLN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.114954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094054 restraints weight = 49256.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096465 restraints weight = 30188.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098015 restraints weight = 21851.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.099244 restraints weight = 17611.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099916 restraints weight = 15089.154| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21476 Z= 0.187 Angle : 0.813 12.163 29036 Z= 0.411 Chirality : 0.044 0.176 3292 Planarity : 0.005 0.066 3616 Dihedral : 8.157 57.926 2828 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.70 % Favored : 87.83 % Rotamer: Outliers : 5.17 % Allowed : 15.28 % 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: -2.62 (0.16), residues: 2556 helix: -0.66 (0.13), residues: 1488 sheet: -1.97 (0.66), residues: 76 loop : -3.45 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 696 TYR 0.021 0.002 TYR B 451 PHE 0.027 0.002 PHE B 666 TRP 0.029 0.002 TRP B 710 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (21472) covalent geometry : angle 0.81278 / 0.41 (29036) hydrogen bonds : bond 0.04032 / 2.66 ( 955) hydrogen bonds : angle 4.74253 / 3.23 ( 2805) Misc. bond : bond 0.00084 / 0.04 ( 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 582 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 464 time to evaluate : 0.865 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 133 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: A 137 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: A 159 MET cc_start: 0.8234 (mmt) cc_final: 0.7914 (mmt) REVERT: A 171 CYS cc_start: 0.8517 (t) cc_final: 0.8246 (t) REVERT: A 191 LEU cc_start: 0.9082 (mt) cc_final: 0.8796 (mt) REVERT: A 195 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 209 THR cc_start: 0.8810 (p) cc_final: 0.8558 (t) REVERT: A 282 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7810 (mmm) REVERT: A 333 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8901 (tt) REVERT: A 336 MET cc_start: 0.8686 (ttm) cc_final: 0.8471 (ttm) REVERT: A 430 HIS cc_start: 0.8700 (t-90) cc_final: 0.8305 (t70) REVERT: A 529 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 555 MET cc_start: 0.8330 (ptp) cc_final: 0.8124 (ptp) REVERT: A 631 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7657 (tm-30) REVERT: A 634 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8578 (mttm) REVERT: B 123 ILE cc_start: 0.9249 (mt) cc_final: 0.9012 (tt) REVERT: B 133 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: B 137 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: B 209 THR cc_start: 0.8788 (p) cc_final: 0.8517 (t) REVERT: B 288 ASP cc_start: 0.8619 (t0) cc_final: 0.7997 (p0) REVERT: B 290 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8845 (p) REVERT: B 346 GLN cc_start: 0.8753 (mt0) cc_final: 0.8144 (mt0) REVERT: B 430 HIS cc_start: 0.8574 (t-90) cc_final: 0.8221 (t70) REVERT: B 555 MET cc_start: 0.8375 (ptp) cc_final: 0.8150 (ptp) REVERT: B 572 MET cc_start: 0.8892 (tpp) cc_final: 0.8584 (tpp) REVERT: B 631 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7389 (tp30) REVERT: C 133 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: C 159 MET cc_start: 0.8210 (mmt) cc_final: 0.7922 (mmt) REVERT: C 209 THR cc_start: 0.8704 (p) cc_final: 0.8464 (t) REVERT: C 282 MET cc_start: 0.7878 (mmm) cc_final: 0.7625 (mmm) REVERT: C 288 ASP cc_start: 0.8526 (t0) cc_final: 0.7891 (p0) REVERT: C 290 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8787 (p) REVERT: C 291 SER cc_start: 0.8969 (t) cc_final: 0.8465 (p) REVERT: C 333 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8982 (tt) REVERT: C 529 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8739 (tm-30) REVERT: C 572 MET cc_start: 0.8927 (tpp) cc_final: 0.8600 (tpp) REVERT: C 631 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7617 (tm-30) REVERT: D 137 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8723 (pm20) REVERT: D 159 MET cc_start: 0.8181 (mmt) cc_final: 0.7853 (mmt) REVERT: D 191 LEU cc_start: 0.9083 (mt) cc_final: 0.8811 (mt) REVERT: D 195 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7872 (mt-10) REVERT: D 209 THR cc_start: 0.8688 (p) cc_final: 0.8476 (t) REVERT: D 288 ASP cc_start: 0.8358 (t0) cc_final: 0.7924 (p0) REVERT: D 290 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8723 (p) REVERT: D 291 SER cc_start: 0.8785 (t) cc_final: 0.8351 (p) REVERT: D 305 THR cc_start: 0.9184 (p) cc_final: 0.8979 (t) REVERT: D 430 HIS cc_start: 0.8647 (t-90) cc_final: 0.8301 (t70) REVERT: D 529 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8661 (tm-30) REVERT: D 555 MET cc_start: 0.8352 (ptp) cc_final: 0.8145 (ptp) REVERT: D 562 MET cc_start: 0.8905 (mmm) cc_final: 0.8640 (mmp) REVERT: D 631 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7645 (tm-30) outliers start: 118 outliers final: 61 residues processed: 542 average time/residue: 0.1373 time to fit residues: 119.7142 Evaluate side-chains 476 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 402 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 200 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 333 LEU 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 427 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 537 VAL 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 665 THR Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 GLU 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 289 ILE 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 427 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 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 748 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 200 LEU 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 333 LEU Chi-restraints excluded: chain C residue 370 LEU 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 537 VAL Chi-restraints excluded: chain C residue 539 LEU 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 717 MET Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 290 THR 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 414 ASP Chi-restraints excluded: chain D residue 427 THR 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 537 VAL 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 665 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 190 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN B 314 ASN B 750 ASN C 314 ASN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095330 restraints weight = 48761.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097806 restraints weight = 30171.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099541 restraints weight = 21691.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100656 restraints weight = 17289.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101452 restraints weight = 14902.486| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21476 Z= 0.156 Angle : 0.771 13.038 29036 Z= 0.387 Chirality : 0.043 0.181 3292 Planarity : 0.004 0.058 3616 Dihedral : 7.685 52.836 2826 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.47 % Allowed : 12.44 % Favored : 87.09 % Rotamer: Outliers : 4.29 % Allowed : 19.26 % Favored : 76.44 % 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: -2.14 (0.16), residues: 2556 helix: -0.19 (0.13), residues: 1484 sheet: -1.90 (0.66), residues: 76 loop : -3.37 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 371 TYR 0.022 0.002 TYR C 451 PHE 0.024 0.002 PHE D 666 TRP 0.018 0.002 TRP B 481 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (21472) covalent geometry : angle 0.77103 / 0.39 (29036) hydrogen bonds : bond 0.03691 / 2.43 ( 955) hydrogen bonds : angle 4.56332 / 3.11 ( 2805) Misc. bond : bond 0.00089 / 0.04 ( 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 522 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 424 time to evaluate : 0.830 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: 0.8422 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: A 159 MET cc_start: 0.8246 (mmt) cc_final: 0.7812 (mmt) REVERT: A 171 CYS cc_start: 0.8487 (t) cc_final: 0.8240 (t) REVERT: A 191 LEU cc_start: 0.9070 (mt) cc_final: 0.8670 (mt) REVERT: A 209 THR cc_start: 0.8658 (p) cc_final: 0.8423 (t) REVERT: A 282 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7842 (mmm) REVERT: A 333 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 446 CYS cc_start: 0.8621 (m) cc_final: 0.8193 (m) REVERT: A 529 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 555 MET cc_start: 0.8270 (ptp) cc_final: 0.8066 (ptp) REVERT: A 562 MET cc_start: 0.9031 (mmm) cc_final: 0.8329 (mmm) REVERT: A 631 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7633 (tm-30) REVERT: A 634 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8451 (mttm) REVERT: B 123 ILE cc_start: 0.9166 (mt) cc_final: 0.8965 (tt) REVERT: B 133 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 137 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8766 (pm20) REVERT: B 159 MET cc_start: 0.8275 (mmt) cc_final: 0.7903 (mpp) REVERT: B 209 THR cc_start: 0.8742 (p) cc_final: 0.8490 (t) REVERT: B 257 GLU cc_start: 0.7200 (tt0) cc_final: 0.6950 (mt-10) REVERT: B 282 MET cc_start: 0.8002 (mmm) cc_final: 0.7721 (mmm) REVERT: B 288 ASP cc_start: 0.8644 (t0) cc_final: 0.8042 (p0) REVERT: B 290 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8664 (p) REVERT: B 346 GLN cc_start: 0.8733 (mt0) cc_final: 0.8125 (mt0) REVERT: B 436 PHE cc_start: 0.7781 (t80) cc_final: 0.7536 (t80) REVERT: B 555 MET cc_start: 0.8384 (ptp) cc_final: 0.8093 (ptp) REVERT: B 572 MET cc_start: 0.8898 (tpp) cc_final: 0.8691 (tpp) REVERT: B 596 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8822 (tp) REVERT: C 133 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 137 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: C 159 MET cc_start: 0.8115 (mmt) cc_final: 0.7747 (mmt) REVERT: C 209 THR cc_start: 0.8633 (p) cc_final: 0.8393 (t) REVERT: C 282 MET cc_start: 0.7918 (mmm) cc_final: 0.7602 (mmm) REVERT: C 288 ASP cc_start: 0.8655 (t0) cc_final: 0.7666 (p0) REVERT: C 290 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8831 (p) REVERT: C 291 SER cc_start: 0.9045 (t) cc_final: 0.8679 (p) REVERT: C 333 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8936 (tt) REVERT: C 479 MET cc_start: 0.6800 (mpp) cc_final: 0.5964 (mpp) REVERT: C 529 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8674 (tm-30) REVERT: C 572 MET cc_start: 0.8957 (tpp) cc_final: 0.8707 (tpp) REVERT: C 587 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 631 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7729 (tm-30) REVERT: C 722 LYS cc_start: 0.7253 (mttt) cc_final: 0.6933 (mtpp) REVERT: D 159 MET cc_start: 0.8215 (mmt) cc_final: 0.7805 (mmt) REVERT: D 171 CYS cc_start: 0.8808 (t) cc_final: 0.8323 (t) REVERT: D 209 THR cc_start: 0.8600 (p) cc_final: 0.8393 (t) REVERT: D 289 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8949 (tp) REVERT: D 290 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8491 (p) REVERT: D 291 SER cc_start: 0.8860 (t) cc_final: 0.8316 (p) REVERT: D 305 THR cc_start: 0.9167 (p) cc_final: 0.8954 (t) REVERT: D 346 GLN cc_start: 0.8728 (mt0) cc_final: 0.8173 (mt0) REVERT: D 479 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6826 (mtm) REVERT: D 529 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8778 (tm-30) REVERT: D 555 MET cc_start: 0.8346 (ptp) cc_final: 0.8097 (ptp) REVERT: D 587 VAL cc_start: 0.9231 (OUTLIER) cc_final: 0.9010 (t) REVERT: D 610 GLU cc_start: 0.6935 (tp30) cc_final: 0.6642 (tp30) REVERT: D 631 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7716 (tm-30) outliers start: 98 outliers final: 45 residues processed: 487 average time/residue: 0.1375 time to fit residues: 107.1017 Evaluate side-chains 442 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 380 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 282 MET Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 453 ILE 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 665 THR 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 133 GLU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 200 LEU 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 588 LEU Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 665 THR 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 133 GLU Chi-restraints excluded: chain C residue 137 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 333 LEU Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 579 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 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 289 ILE 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 484 LEU Chi-restraints excluded: chain D residue 587 VAL 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 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: 4.9990 chunk 221 optimal weight: 0.0270 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 227 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 184 optimal weight: 0.0970 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** 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 = 0.3637 r_free = 0.3637 target = 0.118571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097453 restraints weight = 48518.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099858 restraints weight = 30250.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101497 restraints weight = 21985.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.102611 restraints weight = 17701.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.103350 restraints weight = 15319.696| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21476 Z= 0.135 Angle : 0.754 12.517 29036 Z= 0.374 Chirality : 0.043 0.197 3292 Planarity : 0.004 0.054 3616 Dihedral : 7.212 53.216 2820 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.05 % Favored : 87.60 % Rotamer: Outliers : 3.90 % Allowed : 20.62 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: 0.01 (0.13), residues: 1500 sheet: -1.99 (0.65), residues: 76 loop : -3.29 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.021 0.001 TYR C 451 PHE 0.023 0.001 PHE D 193 TRP 0.020 0.001 TRP C 710 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (21472) covalent geometry : angle 0.75449 / 0.37 (29036) hydrogen bonds : bond 0.03449 / 2.26 ( 955) hydrogen bonds : angle 4.47556 / 3.07 ( 2805) Misc. bond : bond 0.00091 / 0.05 ( 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 538 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 449 time to evaluate : 0.807 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: 0.8147 (mmt) cc_final: 0.7699 (mmt) REVERT: A 171 CYS cc_start: 0.8449 (t) cc_final: 0.8170 (t) REVERT: A 282 MET cc_start: 0.8126 (mtp) cc_final: 0.7916 (mmm) REVERT: A 419 MET cc_start: 0.8240 (mtt) cc_final: 0.8039 (mtt) REVERT: A 446 CYS cc_start: 0.8532 (m) cc_final: 0.8077 (m) REVERT: A 479 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6139 (mpp) REVERT: A 529 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8799 (tm-30) REVERT: A 555 MET cc_start: 0.8272 (ptp) cc_final: 0.8017 (ptp) REVERT: A 596 LEU cc_start: 0.8996 (tt) cc_final: 0.8771 (tp) REVERT: A 616 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.6988 (pttm) REVERT: A 634 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8445 (mttm) REVERT: A 722 LYS cc_start: 0.6609 (mttt) cc_final: 0.6384 (mttm) REVERT: B 137 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: B 171 CYS cc_start: 0.8689 (t) cc_final: 0.8190 (t) REVERT: B 209 THR cc_start: 0.8655 (p) cc_final: 0.8367 (t) REVERT: B 257 GLU cc_start: 0.7188 (tt0) cc_final: 0.6942 (mt-10) REVERT: B 282 MET cc_start: 0.7920 (mmm) cc_final: 0.7643 (mmm) REVERT: B 288 ASP cc_start: 0.8656 (t0) cc_final: 0.8007 (p0) REVERT: B 290 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8609 (p) REVERT: B 419 MET cc_start: 0.8495 (mtt) cc_final: 0.8274 (mtt) REVERT: B 446 CYS cc_start: 0.8520 (m) cc_final: 0.8081 (m) REVERT: B 555 MET cc_start: 0.8337 (ptp) cc_final: 0.7984 (ptp) REVERT: B 596 LEU cc_start: 0.9017 (tt) cc_final: 0.8795 (tp) REVERT: C 133 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: C 159 MET cc_start: 0.8187 (mmt) cc_final: 0.7791 (mmt) REVERT: C 171 CYS cc_start: 0.8742 (t) cc_final: 0.8244 (t) REVERT: C 209 THR cc_start: 0.8562 (p) cc_final: 0.8360 (t) REVERT: C 282 MET cc_start: 0.7938 (mmm) cc_final: 0.7583 (mmm) REVERT: C 288 ASP cc_start: 0.8657 (t0) cc_final: 0.8427 (t0) REVERT: C 290 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 291 SER cc_start: 0.8991 (t) cc_final: 0.8612 (p) REVERT: C 346 GLN cc_start: 0.8738 (mt0) cc_final: 0.8232 (mt0) REVERT: C 446 CYS cc_start: 0.8589 (m) cc_final: 0.8127 (m) REVERT: C 479 MET cc_start: 0.6420 (mpp) cc_final: 0.5718 (mpp) REVERT: C 529 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8780 (tm-30) REVERT: C 555 MET cc_start: 0.8291 (ptp) cc_final: 0.8081 (ptp) REVERT: C 572 MET cc_start: 0.8920 (tpp) cc_final: 0.8688 (tpp) REVERT: C 631 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7716 (tm-30) REVERT: D 159 MET cc_start: 0.8139 (mmt) cc_final: 0.7700 (mmt) REVERT: D 171 CYS cc_start: 0.8779 (t) cc_final: 0.8263 (t) REVERT: D 290 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8392 (p) REVERT: D 305 THR cc_start: 0.9191 (p) cc_final: 0.8958 (t) REVERT: D 346 GLN cc_start: 0.8675 (mt0) cc_final: 0.8188 (mt0) REVERT: D 419 MET cc_start: 0.8284 (mtt) cc_final: 0.8071 (mtt) REVERT: D 529 GLN cc_start: 0.9182 (tm-30) cc_final: 0.8901 (tm-30) REVERT: D 555 MET cc_start: 0.8303 (ptp) cc_final: 0.7847 (ptp) REVERT: D 610 GLU cc_start: 0.6783 (tp30) cc_final: 0.6505 (tp30) REVERT: D 616 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7262 (pttm) outliers start: 89 outliers final: 31 residues processed: 500 average time/residue: 0.1346 time to fit residues: 108.9011 Evaluate side-chains 432 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 392 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 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 484 LEU Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 153 ASP 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 684 VAL Chi-restraints excluded: chain B residue 748 PHE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 153 ASP 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 484 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 616 LYS Chi-restraints excluded: chain D residue 707 LEU 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: 0.9980 chunk 13 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 0.0000 chunk 239 optimal weight: 7.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN B 750 ASN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.117443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096625 restraints weight = 48371.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099052 restraints weight = 29780.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100570 restraints weight = 21364.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101806 restraints weight = 17223.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102509 restraints weight = 14727.035| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21476 Z= 0.144 Angle : 0.766 12.261 29036 Z= 0.380 Chirality : 0.043 0.159 3292 Planarity : 0.004 0.061 3616 Dihedral : 7.106 55.610 2820 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.56 % Favored : 87.13 % Rotamer: Outliers : 3.55 % Allowed : 22.77 % 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: -1.75 (0.17), residues: 2556 helix: 0.12 (0.13), residues: 1496 sheet: -2.38 (0.59), residues: 76 loop : -3.16 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 371 TYR 0.020 0.002 TYR C 451 PHE 0.027 0.001 PHE B 666 TRP 0.025 0.002 TRP B 710 HIS 0.002 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (21472) covalent geometry : angle 0.76639 / 0.38 (29036) hydrogen bonds : bond 0.03455 / 2.28 ( 955) hydrogen bonds : angle 4.48086 / 3.08 ( 2805) Misc. bond : bond 0.00064 / 0.03 ( 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 496 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 415 time to evaluate : 0.874 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 159 MET cc_start: 0.8238 (mmt) cc_final: 0.7736 (mmt) REVERT: A 171 CYS cc_start: 0.8472 (t) cc_final: 0.8265 (t) REVERT: A 282 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7978 (mmm) REVERT: A 419 MET cc_start: 0.8316 (mtt) cc_final: 0.8096 (mtt) REVERT: A 446 CYS cc_start: 0.8553 (m) cc_final: 0.8095 (m) REVERT: A 479 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6129 (mpp) REVERT: A 529 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8787 (tm-30) REVERT: A 555 MET cc_start: 0.8333 (ptp) cc_final: 0.7829 (ptp) REVERT: A 562 MET cc_start: 0.8940 (mmm) cc_final: 0.8328 (mmm) REVERT: A 616 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7058 (pttm) REVERT: A 634 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8322 (mttm) REVERT: A 722 LYS cc_start: 0.6553 (mttt) cc_final: 0.6154 (mtpp) REVERT: B 133 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7971 (mp0) REVERT: B 137 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8810 (pm20) REVERT: B 159 MET cc_start: 0.8065 (mmt) cc_final: 0.7757 (mmt) REVERT: B 171 CYS cc_start: 0.8753 (t) cc_final: 0.8242 (t) REVERT: B 209 THR cc_start: 0.8659 (p) cc_final: 0.8409 (t) REVERT: B 288 ASP cc_start: 0.8634 (t0) cc_final: 0.7894 (p0) REVERT: B 290 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8671 (p) REVERT: B 346 GLN cc_start: 0.8799 (mt0) cc_final: 0.8252 (mt0) REVERT: B 419 MET cc_start: 0.8588 (mtt) cc_final: 0.8361 (mtt) REVERT: B 446 CYS cc_start: 0.8509 (m) cc_final: 0.8071 (m) REVERT: B 555 MET cc_start: 0.8437 (ptp) cc_final: 0.7913 (ptp) REVERT: B 561 ASN cc_start: 0.8865 (t0) cc_final: 0.7910 (t0) REVERT: B 572 MET cc_start: 0.8704 (tpp) cc_final: 0.8503 (tpp) REVERT: B 710 TRP cc_start: 0.7155 (OUTLIER) cc_final: 0.6905 (p-90) REVERT: C 133 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: C 159 MET cc_start: 0.8178 (mmt) cc_final: 0.7713 (mmt) REVERT: C 171 CYS cc_start: 0.8783 (t) cc_final: 0.8272 (t) REVERT: C 209 THR cc_start: 0.8589 (p) cc_final: 0.8364 (t) REVERT: C 216 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8217 (tp40) REVERT: C 220 ASN cc_start: 0.9013 (t0) cc_final: 0.8702 (t0) REVERT: C 282 MET cc_start: 0.7946 (mmm) cc_final: 0.7625 (mmm) REVERT: C 288 ASP cc_start: 0.8705 (t0) cc_final: 0.8432 (t0) REVERT: C 290 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8699 (p) REVERT: C 291 SER cc_start: 0.9026 (t) cc_final: 0.8726 (p) REVERT: C 346 GLN cc_start: 0.8785 (mt0) cc_final: 0.8250 (mt0) REVERT: C 446 CYS cc_start: 0.8570 (m) cc_final: 0.8086 (m) REVERT: C 479 MET cc_start: 0.6452 (mpp) cc_final: 0.5786 (mpp) REVERT: C 529 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8772 (tm-30) REVERT: C 555 MET cc_start: 0.8367 (ptp) cc_final: 0.8145 (ptp) REVERT: C 561 ASN cc_start: 0.8720 (m-40) cc_final: 0.8128 (t0) REVERT: C 572 MET cc_start: 0.9007 (tpp) cc_final: 0.8719 (tpp) REVERT: C 598 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9125 (tp) REVERT: C 631 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7826 (tm-30) REVERT: C 722 LYS cc_start: 0.6604 (mttt) cc_final: 0.6331 (mmtt) REVERT: D 159 MET cc_start: 0.8203 (mmt) cc_final: 0.7717 (mmt) REVERT: D 171 CYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8276 (t) REVERT: D 282 MET cc_start: 0.8104 (mmm) cc_final: 0.7812 (tpp) REVERT: D 346 GLN cc_start: 0.8727 (mt0) cc_final: 0.8058 (mp10) REVERT: D 357 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9494 (tt) REVERT: D 479 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6125 (mpp) REVERT: D 529 GLN cc_start: 0.9180 (tm-30) cc_final: 0.8784 (tm-30) REVERT: D 555 MET cc_start: 0.8457 (ptp) cc_final: 0.7970 (ptp) REVERT: D 610 GLU cc_start: 0.6802 (tp30) cc_final: 0.6514 (tp30) REVERT: D 616 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7203 (pttm) outliers start: 81 outliers final: 39 residues processed: 469 average time/residue: 0.1383 time to fit residues: 105.5676 Evaluate side-chains 432 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 377 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 282 MET 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 592 PHE Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 137 GLU 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 624 SER 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 133 GLU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 216 GLN 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 453 ILE Chi-restraints excluded: chain C residue 476 THR 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 707 LEU Chi-restraints excluded: chain C residue 748 PHE Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 357 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 616 LYS Chi-restraints excluded: chain D residue 707 LEU 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: 5.9990 chunk 45 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099023 restraints weight = 48417.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101466 restraints weight = 29800.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103141 restraints weight = 21369.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104275 restraints weight = 17075.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.104935 restraints weight = 14687.161| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6264 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= 0.133 Angle : 0.767 12.097 29036 Z= 0.377 Chirality : 0.043 0.347 3292 Planarity : 0.004 0.063 3616 Dihedral : 6.962 53.296 2820 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.28 % Favored : 87.40 % Rotamer: Outliers : 3.55 % Allowed : 23.03 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.46 (0.17), residues: 2556 helix: 0.32 (0.14), residues: 1476 sheet: -2.47 (0.58), residues: 72 loop : -2.88 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 371 TYR 0.022 0.001 TYR A 661 PHE 0.026 0.001 PHE B 666 TRP 0.023 0.001 TRP C 710 HIS 0.002 0.001 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21472) covalent geometry : angle 0.76715 / 0.38 (29036) hydrogen bonds : bond 0.03272 / 2.16 ( 955) hydrogen bonds : angle 4.44981 / 3.06 ( 2805) Misc. bond : bond 0.00075 / 0.04 ( 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 488 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 407 time to evaluate : 0.868 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: 0.8178 (mmt) cc_final: 0.7733 (mmt) REVERT: A 282 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8022 (mmm) REVERT: A 346 GLN cc_start: 0.8760 (mt0) cc_final: 0.8227 (mt0) REVERT: A 419 MET cc_start: 0.8265 (mtt) cc_final: 0.8051 (mtt) REVERT: A 446 CYS cc_start: 0.8454 (m) cc_final: 0.8001 (m) REVERT: A 479 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6119 (mpp) REVERT: A 529 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8746 (tm-30) REVERT: A 555 MET cc_start: 0.8208 (ptp) cc_final: 0.7855 (ptp) REVERT: A 562 MET cc_start: 0.8861 (mmm) cc_final: 0.8246 (mmm) REVERT: A 596 LEU cc_start: 0.9003 (tt) cc_final: 0.8721 (tp) REVERT: A 616 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7182 (pttm) REVERT: A 634 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8312 (mttp) REVERT: A 656 PHE cc_start: 0.8478 (m-10) cc_final: 0.8196 (m-80) REVERT: A 722 LYS cc_start: 0.6179 (mttt) cc_final: 0.5902 (mttm) REVERT: A 748 PHE cc_start: 0.6547 (OUTLIER) cc_final: 0.5931 (m-80) REVERT: B 133 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: B 159 MET cc_start: 0.8141 (mmt) cc_final: 0.7824 (mmt) REVERT: B 171 CYS cc_start: 0.8724 (t) cc_final: 0.8222 (t) REVERT: B 282 MET cc_start: 0.7993 (mmm) cc_final: 0.7781 (mmm) REVERT: B 290 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8690 (p) REVERT: B 360 ILE cc_start: 0.9378 (mt) cc_final: 0.9142 (tp) REVERT: B 419 MET cc_start: 0.8574 (mtt) cc_final: 0.8325 (mtt) REVERT: B 446 CYS cc_start: 0.8397 (m) cc_final: 0.7919 (m) REVERT: B 555 MET cc_start: 0.8348 (ptp) cc_final: 0.8004 (ptp) REVERT: B 561 ASN cc_start: 0.8865 (t0) cc_final: 0.7981 (t0) REVERT: B 710 TRP cc_start: 0.7154 (OUTLIER) cc_final: 0.6937 (t-100) REVERT: C 159 MET cc_start: 0.8119 (mmt) cc_final: 0.7673 (mmt) REVERT: C 282 MET cc_start: 0.7929 (mmm) cc_final: 0.7725 (mmm) REVERT: C 288 ASP cc_start: 0.8710 (t0) cc_final: 0.8425 (t0) REVERT: C 290 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8673 (p) REVERT: C 291 SER cc_start: 0.8837 (t) cc_final: 0.8612 (p) REVERT: C 346 GLN cc_start: 0.8685 (mt0) cc_final: 0.8136 (mp10) REVERT: C 446 CYS cc_start: 0.8499 (m) cc_final: 0.7937 (m) REVERT: C 479 MET cc_start: 0.6429 (mpp) cc_final: 0.5956 (mpp) REVERT: C 529 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8729 (tm-30) REVERT: C 555 MET cc_start: 0.8302 (ptp) cc_final: 0.8079 (ptp) REVERT: C 561 ASN cc_start: 0.8640 (m-40) cc_final: 0.8092 (t0) REVERT: C 572 MET cc_start: 0.8959 (tpp) cc_final: 0.8677 (tpp) REVERT: C 598 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9079 (tp) REVERT: C 632 LEU cc_start: 0.9269 (tt) cc_final: 0.8966 (tp) REVERT: D 159 MET cc_start: 0.8155 (mmt) cc_final: 0.7675 (mmt) REVERT: D 171 CYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8175 (t) REVERT: D 282 MET cc_start: 0.8090 (mmm) cc_final: 0.7716 (mmp) REVERT: D 346 GLN cc_start: 0.8712 (mt0) cc_final: 0.8038 (mp10) REVERT: D 479 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6074 (mpp) REVERT: D 529 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8743 (tm-30) REVERT: D 538 PHE cc_start: 0.8134 (m-80) cc_final: 0.7724 (m-10) REVERT: D 555 MET cc_start: 0.8395 (ptp) cc_final: 0.8102 (ptp) REVERT: D 610 GLU cc_start: 0.6783 (tp30) cc_final: 0.6459 (tp30) REVERT: D 656 PHE cc_start: 0.8300 (m-10) cc_final: 0.8080 (m-80) REVERT: D 702 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7619 (mm-30) outliers start: 81 outliers final: 33 residues processed: 455 average time/residue: 0.1377 time to fit residues: 101.4982 Evaluate side-chains 407 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 282 MET 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 672 MET Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain B residue 133 GLU 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 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 624 SER 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 C residue 153 ASP Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 453 ILE 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 672 MET Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS 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 707 LEU 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: 0.8980 chunk 188 optimal weight: 0.0270 chunk 133 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 212 optimal weight: 0.0870 chunk 220 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 220 ASN ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 645 GLN D 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099778 restraints weight = 48301.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.102211 restraints weight = 29788.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.103864 restraints weight = 21459.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104871 restraints weight = 17186.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105691 restraints weight = 14886.165| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21476 Z= 0.130 Angle : 0.778 12.360 29036 Z= 0.379 Chirality : 0.043 0.332 3292 Planarity : 0.004 0.047 3616 Dihedral : 6.851 52.204 2820 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.09 % Favored : 87.60 % Rotamer: Outliers : 3.15 % Allowed : 23.69 % Favored : 73.16 % 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: -1.36 (0.17), residues: 2556 helix: 0.40 (0.14), residues: 1468 sheet: -2.73 (0.55), residues: 76 loop : -2.78 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.022 0.001 TYR B 359 PHE 0.035 0.001 PHE B 748 TRP 0.023 0.001 TRP D 710 HIS 0.002 0.000 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21472) covalent geometry : angle 0.77785 / 0.38 (29036) hydrogen bonds : bond 0.03247 / 2.15 ( 955) hydrogen bonds : angle 4.42125 / 3.03 ( 2805) Misc. bond : bond 0.00065 / 0.03 ( 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 478 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 406 time to evaluate : 0.822 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: 0.8217 (mmt) cc_final: 0.7812 (mmt) REVERT: A 282 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.8009 (mmm) REVERT: A 419 MET cc_start: 0.8238 (mtt) cc_final: 0.7954 (mtt) REVERT: A 446 CYS cc_start: 0.8327 (m) cc_final: 0.7810 (m) REVERT: A 479 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6662 (mpp) REVERT: A 529 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 538 PHE cc_start: 0.8045 (m-80) cc_final: 0.7668 (m-10) REVERT: A 555 MET cc_start: 0.8145 (ptp) cc_final: 0.7781 (ptp) REVERT: A 562 MET cc_start: 0.8813 (mmm) cc_final: 0.8097 (mmm) REVERT: A 596 LEU cc_start: 0.8990 (tt) cc_final: 0.8734 (tp) REVERT: A 634 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8168 (mttp) REVERT: A 656 PHE cc_start: 0.8381 (m-10) cc_final: 0.8050 (m-80) REVERT: B 159 MET cc_start: 0.8084 (mmt) cc_final: 0.7723 (mmt) REVERT: B 282 MET cc_start: 0.7997 (mmm) cc_final: 0.7780 (mmm) REVERT: B 288 ASP cc_start: 0.8428 (t0) cc_final: 0.7933 (p0) REVERT: B 290 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 419 MET cc_start: 0.8536 (mtt) cc_final: 0.8325 (mtt) REVERT: B 538 PHE cc_start: 0.8047 (m-80) cc_final: 0.7649 (m-10) REVERT: B 555 MET cc_start: 0.8270 (ptp) cc_final: 0.7986 (ptp) REVERT: B 561 ASN cc_start: 0.8805 (t0) cc_final: 0.7998 (t0) REVERT: B 596 LEU cc_start: 0.9148 (tt) cc_final: 0.8746 (tp) REVERT: C 159 MET cc_start: 0.8135 (mmt) cc_final: 0.7676 (mmt) REVERT: C 282 MET cc_start: 0.7933 (mmm) cc_final: 0.7719 (mmm) REVERT: C 288 ASP cc_start: 0.8722 (t0) cc_final: 0.8271 (t0) REVERT: C 290 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 479 MET cc_start: 0.6380 (mpp) cc_final: 0.5890 (mpp) REVERT: C 532 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9241 (tp) REVERT: C 538 PHE cc_start: 0.8118 (m-80) cc_final: 0.7709 (m-10) REVERT: C 561 ASN cc_start: 0.8629 (m-40) cc_final: 0.8041 (t0) REVERT: C 572 MET cc_start: 0.8821 (tpp) cc_final: 0.8567 (tpp) REVERT: C 596 LEU cc_start: 0.9275 (tt) cc_final: 0.8835 (mt) REVERT: C 598 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9092 (tp) REVERT: D 159 MET cc_start: 0.8140 (mmt) cc_final: 0.7660 (mmt) REVERT: D 171 CYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8144 (t) REVERT: D 479 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.5981 (mpp) REVERT: D 529 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8674 (tm-30) REVERT: D 538 PHE cc_start: 0.8065 (m-80) cc_final: 0.7661 (m-10) REVERT: D 555 MET cc_start: 0.8327 (ptp) cc_final: 0.8048 (ptp) REVERT: D 610 GLU cc_start: 0.6666 (tp30) cc_final: 0.6391 (tp30) REVERT: D 656 PHE cc_start: 0.8282 (m-10) cc_final: 0.8039 (m-80) outliers start: 72 outliers final: 36 residues processed: 453 average time/residue: 0.1390 time to fit residues: 101.6482 Evaluate side-chains 403 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 358 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 282 MET 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 592 PHE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 672 MET 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 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 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 532 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS 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 704 GLU Chi-restraints excluded: chain D residue 707 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 166 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 195 optimal weight: 8.9990 chunk 99 optimal weight: 0.0970 chunk 229 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 HIS ** 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 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.121216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100158 restraints weight = 48769.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102576 restraints weight = 30653.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104250 restraints weight = 22355.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105249 restraints weight = 18055.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106058 restraints weight = 15721.528| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21476 Z= 0.134 Angle : 0.799 13.845 29036 Z= 0.388 Chirality : 0.043 0.308 3292 Planarity : 0.004 0.089 3616 Dihedral : 6.820 52.699 2820 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.93 % Favored : 87.75 % Rotamer: Outliers : 2.28 % Allowed : 25.26 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.35 (0.17), residues: 2556 helix: 0.41 (0.14), residues: 1468 sheet: -2.79 (0.55), residues: 76 loop : -2.79 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 733 TYR 0.022 0.002 TYR D 661 PHE 0.046 0.001 PHE A 748 TRP 0.020 0.001 TRP B 742 HIS 0.002 0.000 HIS D 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (21472) covalent geometry : angle 0.79927 / 0.39 (29036) hydrogen bonds : bond 0.03243 / 2.12 ( 955) hydrogen bonds : angle 4.40421 / 3.02 ( 2805) Misc. bond : bond 0.00062 / 0.03 ( 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 434 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 382 time to evaluate : 0.942 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: 0.8190 (mmt) cc_final: 0.7790 (mmt) REVERT: A 257 GLU cc_start: 0.7539 (tt0) cc_final: 0.7265 (mt-10) REVERT: A 282 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7859 (mmm) REVERT: A 446 CYS cc_start: 0.8443 (m) cc_final: 0.7970 (m) REVERT: A 479 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6796 (mpp) REVERT: A 529 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8707 (tm-30) REVERT: A 538 PHE cc_start: 0.8055 (m-80) cc_final: 0.7705 (m-10) REVERT: A 562 MET cc_start: 0.8847 (mmm) cc_final: 0.8154 (mmm) REVERT: A 596 LEU cc_start: 0.8997 (tt) cc_final: 0.8719 (tp) REVERT: A 634 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (mttp) REVERT: A 656 PHE cc_start: 0.8342 (m-10) cc_final: 0.8024 (m-80) REVERT: B 159 MET cc_start: 0.8033 (mmt) cc_final: 0.7665 (mmt) REVERT: B 257 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6323 (mm-30) REVERT: B 288 ASP cc_start: 0.8414 (t0) cc_final: 0.7823 (p0) REVERT: B 290 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 419 MET cc_start: 0.8511 (mtt) cc_final: 0.8307 (mtt) REVERT: B 538 PHE cc_start: 0.8029 (m-80) cc_final: 0.7669 (m-10) REVERT: B 555 MET cc_start: 0.8234 (ptp) cc_final: 0.7965 (ptp) REVERT: B 561 ASN cc_start: 0.8701 (t0) cc_final: 0.8006 (t0) REVERT: B 564 TYR cc_start: 0.8446 (t80) cc_final: 0.8211 (t80) REVERT: B 596 LEU cc_start: 0.9154 (tt) cc_final: 0.8773 (tp) REVERT: C 159 MET cc_start: 0.8105 (mmt) cc_final: 0.7662 (mmt) REVERT: C 290 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8824 (p) REVERT: C 479 MET cc_start: 0.6434 (mpp) cc_final: 0.5993 (mpp) REVERT: C 538 PHE cc_start: 0.7962 (m-80) cc_final: 0.7599 (m-10) REVERT: C 561 ASN cc_start: 0.8561 (m-40) cc_final: 0.8042 (t0) REVERT: C 598 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9098 (tp) REVERT: C 677 MET cc_start: 0.7121 (mmm) cc_final: 0.6799 (mmt) REVERT: D 159 MET cc_start: 0.8095 (mmt) cc_final: 0.7622 (mmt) REVERT: D 479 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6019 (mpp) REVERT: D 538 PHE cc_start: 0.8019 (m-80) cc_final: 0.7644 (m-10) REVERT: D 555 MET cc_start: 0.8301 (ptp) cc_final: 0.8082 (ptp) REVERT: D 610 GLU cc_start: 0.6677 (tp30) cc_final: 0.6348 (tp30) REVERT: D 656 PHE cc_start: 0.8255 (m-10) cc_final: 0.8013 (m-80) outliers start: 52 outliers final: 38 residues processed: 415 average time/residue: 0.1369 time to fit residues: 92.5440 Evaluate side-chains 397 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 352 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 282 MET 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 592 PHE Chi-restraints excluded: chain A residue 634 LYS 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 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 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 742 TRP 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 290 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS 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 704 GLU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 88 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 116 optimal weight: 0.0050 chunk 74 optimal weight: 0.6980 chunk 192 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 HIS A 645 GLN ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 HIS ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101269 restraints weight = 48585.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103657 restraints weight = 30967.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105287 restraints weight = 22795.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106407 restraints weight = 18481.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107047 restraints weight = 15980.431| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.7025 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= 0.133 Angle : 0.803 13.612 29036 Z= 0.389 Chirality : 0.043 0.301 3292 Planarity : 0.004 0.053 3616 Dihedral : 6.749 53.540 2820 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.58 % Favored : 88.11 % Rotamer: Outliers : 2.10 % Allowed : 25.57 % Favored : 72.33 % 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: -1.28 (0.17), residues: 2556 helix: 0.48 (0.14), residues: 1480 sheet: -2.84 (0.54), residues: 76 loop : -2.81 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 733 TYR 0.029 0.002 TYR C 254 PHE 0.045 0.001 PHE A 748 TRP 0.019 0.001 TRP A 742 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21472) covalent geometry : angle 0.80266 / 0.39 (29036) hydrogen bonds : bond 0.03150 / 2.06 ( 955) hydrogen bonds : angle 4.37230 / 2.99 ( 2805) Misc. bond : bond 0.00052 / 0.03 ( 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 437 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 389 time to evaluate : 0.819 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: 0.8204 (mmt) cc_final: 0.7807 (mmt) REVERT: A 308 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7068 (mm-30) REVERT: A 419 MET cc_start: 0.8175 (mtt) cc_final: 0.7830 (mtt) REVERT: A 479 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6552 (mpp) REVERT: A 562 MET cc_start: 0.8792 (mmm) cc_final: 0.8130 (mmm) REVERT: A 634 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8393 (mttp) REVERT: A 656 PHE cc_start: 0.8266 (m-10) cc_final: 0.7910 (m-80) REVERT: B 159 MET cc_start: 0.8036 (mmt) cc_final: 0.7695 (mmt) REVERT: B 288 ASP cc_start: 0.8363 (t0) cc_final: 0.7837 (p0) REVERT: B 538 PHE cc_start: 0.8000 (m-80) cc_final: 0.7669 (m-10) REVERT: B 555 MET cc_start: 0.8301 (ptp) cc_final: 0.8008 (ptp) REVERT: B 561 ASN cc_start: 0.8696 (t0) cc_final: 0.8009 (t0) REVERT: B 564 TYR cc_start: 0.8403 (t80) cc_final: 0.8149 (t80) REVERT: C 159 MET cc_start: 0.8120 (mmt) cc_final: 0.7685 (mmt) REVERT: C 282 MET cc_start: 0.8016 (mmm) cc_final: 0.7814 (mmm) REVERT: C 479 MET cc_start: 0.6462 (mpp) cc_final: 0.6066 (mpp) REVERT: C 538 PHE cc_start: 0.7991 (m-80) cc_final: 0.7629 (m-10) REVERT: C 561 ASN cc_start: 0.8533 (m-40) cc_final: 0.8014 (t0) REVERT: C 596 LEU cc_start: 0.8992 (tt) cc_final: 0.8712 (tp) REVERT: C 598 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9113 (tp) REVERT: C 677 MET cc_start: 0.7136 (mmm) cc_final: 0.6924 (mmt) REVERT: D 159 MET cc_start: 0.8090 (mmt) cc_final: 0.7617 (mmt) REVERT: D 171 CYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8218 (t) REVERT: D 479 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6435 (mpp) REVERT: D 538 PHE cc_start: 0.8044 (m-80) cc_final: 0.7602 (m-10) REVERT: D 555 MET cc_start: 0.8305 (ptp) cc_final: 0.8084 (ptp) REVERT: D 561 ASN cc_start: 0.8707 (t0) cc_final: 0.7872 (t0) REVERT: D 610 GLU cc_start: 0.6713 (tp30) cc_final: 0.6428 (tp30) REVERT: D 656 PHE cc_start: 0.8234 (m-10) cc_final: 0.8000 (m-80) outliers start: 48 outliers final: 36 residues processed: 420 average time/residue: 0.1326 time to fit residues: 90.7664 Evaluate side-chains 410 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 369 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 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 592 PHE Chi-restraints excluded: chain A residue 634 LYS 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 742 TRP 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 453 ILE Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 742 TRP 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 453 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 742 TRP Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 171 CYS 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 704 GLU Chi-restraints excluded: chain D residue 710 TRP Chi-restraints excluded: chain D residue 742 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 21 optimal weight: 0.0670 chunk 22 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 chunk 114 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 426 HIS ** D 645 GLN ** 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 = 0.3654 r_free = 0.3654 target = 0.120132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099502 restraints weight = 48197.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101964 restraints weight = 29723.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103554 restraints weight = 21292.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104775 restraints weight = 17040.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105479 restraints weight = 14518.671| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.7203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21476 Z= 0.134 Angle : 0.803 14.089 29036 Z= 0.390 Chirality : 0.043 0.287 3292 Planarity : 0.004 0.047 3616 Dihedral : 6.733 53.277 2820 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.62 % Favored : 88.07 % Rotamer: Outliers : 2.36 % Allowed : 26.23 % Favored : 71.41 % 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: -1.28 (0.17), residues: 2556 helix: 0.49 (0.14), residues: 1480 sheet: -2.84 (0.54), residues: 76 loop : -2.82 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 122 TYR 0.020 0.001 TYR A 451 PHE 0.038 0.001 PHE A 748 TRP 0.019 0.001 TRP D 742 HIS 0.012 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (21472) covalent geometry : angle 0.80349 / 0.39 (29036) hydrogen bonds : bond 0.03121 / 2.04 ( 955) hydrogen bonds : angle 4.40140 / 3.01 ( 2805) Misc. bond : bond 0.00050 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.80 seconds wall clock time: 62 minutes 9.08 seconds (3729.08 seconds total)