Starting phenix.real_space_refine on Fri Mar 6 17:15:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ufs_26479/03_2026/7ufs_26479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ufs_26479/03_2026/7ufs_26479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ufs_26479/03_2026/7ufs_26479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ufs_26479/03_2026/7ufs_26479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ufs_26479/03_2026/7ufs_26479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ufs_26479/03_2026/7ufs_26479.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.889 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 Zn 4 6.06 5 S 140 5.16 5 C 20576 2.51 5 N 5776 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32596 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 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: "B" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 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: "C" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 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: "D" Number of atoms: 8148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8148 Classifications: {'peptide': 1040} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 60, 'TRANS': 979} Chain breaks: 1 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.72, per 1000 atoms: 0.21 Number of scatterers: 32596 At special positions: 0 Unit cell: (164.15, 142.71, 98.49, 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) Zn 4 29.99 S 140 16.00 O 6100 8.00 N 5776 7.00 C 20576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 276 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 598 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 598 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 276 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 598 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 276 " pdb=" ZN D1101 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 598 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 276 " 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7704 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 44 sheets defined 29.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.663A pdb=" N TRP A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.574A pdb=" N ALA A 252 " --> pdb=" O PRO A 248 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 287 through 306 removed outlier: 4.120A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 340 removed outlier: 3.906A pdb=" N GLU A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 376 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 451 through 461 removed outlier: 3.669A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 removed outlier: 3.549A pdb=" N THR A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.535A pdb=" N THR A 545 " --> pdb=" O GLY A 542 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 546 " --> pdb=" O THR A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 606 through 637 removed outlier: 3.673A pdb=" N HIS A 610 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 637 " --> pdb=" O GLN A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.681A pdb=" N SER A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 844 removed outlier: 3.714A pdb=" N ALA A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 935 Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.663A pdb=" N TRP B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.574A pdb=" N ALA B 252 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 287 through 306 removed outlier: 4.120A pdb=" N GLU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 340 removed outlier: 3.906A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 376 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 451 through 461 removed outlier: 3.669A pdb=" N GLN B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 495 removed outlier: 3.548A pdb=" N THR B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.534A pdb=" N THR B 545 " --> pdb=" O GLY B 542 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 546 " --> pdb=" O THR B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 546' Processing helix chain 'B' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 593 through 597 Processing helix chain 'B' and resid 606 through 638 removed outlier: 3.674A pdb=" N HIS B 610 " --> pdb=" O ILE B 606 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 614 " --> pdb=" O HIS B 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU B 637 " --> pdb=" O GLN B 633 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 638 " --> pdb=" O ALA B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 660 removed outlier: 3.681A pdb=" N SER B 660 " --> pdb=" O PRO B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 844 removed outlier: 3.714A pdb=" N ALA B 844 " --> pdb=" O ARG B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 935 Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 44 through 55 Processing helix chain 'C' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 237 removed outlier: 3.663A pdb=" N TRP C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.574A pdb=" N ALA C 252 " --> pdb=" O PRO C 248 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 287 through 306 removed outlier: 4.120A pdb=" N GLU C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR C 319 " --> pdb=" O SER C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 340 removed outlier: 3.905A pdb=" N GLU C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 376 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 451 through 461 removed outlier: 3.669A pdb=" N GLN C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 495 removed outlier: 3.549A pdb=" N THR C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 493 " --> pdb=" O THR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.535A pdb=" N THR C 545 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 546 " --> pdb=" O THR C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS C 551 " --> pdb=" O GLN C 547 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 575 " --> pdb=" O ALA C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 606 through 638 removed outlier: 3.674A pdb=" N HIS C 610 " --> pdb=" O ILE C 606 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG C 614 " --> pdb=" O HIS C 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 637 " --> pdb=" O GLN C 633 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 638 " --> pdb=" O ALA C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.680A pdb=" N SER C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 844 removed outlier: 3.716A pdb=" N ALA C 844 " --> pdb=" O ARG C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 935 Processing helix chain 'D' and resid 4 through 19 removed outlier: 3.680A pdb=" N GLU D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 44 through 55 Processing helix chain 'D' and resid 198 through 218 removed outlier: 3.735A pdb=" N PHE D 202 " --> pdb=" O ASN D 198 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 237 removed outlier: 3.664A pdb=" N TRP D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.573A pdb=" N ALA D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 287 through 306 removed outlier: 4.121A pdb=" N GLU D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 326 removed outlier: 3.705A pdb=" N TYR D 319 " --> pdb=" O SER D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 340 removed outlier: 3.906A pdb=" N GLU D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 376 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 451 through 461 removed outlier: 3.668A pdb=" N GLN D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 495 removed outlier: 3.549A pdb=" N THR D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 493 " --> pdb=" O THR D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 542 through 546 removed outlier: 3.535A pdb=" N THR D 545 " --> pdb=" O GLY D 542 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 546 " --> pdb=" O THR D 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 542 through 546' Processing helix chain 'D' and resid 547 through 575 removed outlier: 3.878A pdb=" N LYS D 551 " --> pdb=" O GLN D 547 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 589 Processing helix chain 'D' and resid 593 through 597 Processing helix chain 'D' and resid 606 through 638 removed outlier: 3.675A pdb=" N HIS D 610 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 614 " --> pdb=" O HIS D 610 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 637 " --> pdb=" O GLN D 633 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 638 " --> pdb=" O ALA D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.680A pdb=" N SER D 660 " --> pdb=" O PRO D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 844 removed outlier: 3.715A pdb=" N ALA D 844 " --> pdb=" O ARG D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 935 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.512A pdb=" N THR A 195 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.645A pdb=" N LEU A 33 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 73 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 114 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS A 124 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.461A pdb=" N GLY A 66 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA A 471 " --> pdb=" O ASN A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 385 removed outlier: 6.638A pdb=" N ILE A 384 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE A 688 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 696 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 706 " --> pdb=" O ARG A 697 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 729 removed outlier: 6.838A pdb=" N LEU A 809 " --> pdb=" O LEU A 896 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY A 872 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 873 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 848 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 762 removed outlier: 3.580A pdb=" N VAL A 773 " --> pdb=" O MET A 756 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS A 771 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 760 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 769 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 768 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 821 through 826 removed outlier: 3.945A pdb=" N GLY A 829 " --> pdb=" O CYS A 826 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 950 through 951 removed outlier: 3.579A pdb=" N ALA A1030 " --> pdb=" O LEU A 989 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 958 through 965 removed outlier: 5.655A pdb=" N LEU A 960 " --> pdb=" O TYR A 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A 978 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A1041 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.512A pdb=" N THR B 195 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 60 through 62 removed outlier: 4.645A pdb=" N LEU B 33 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 73 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 114 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 124 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 66 through 67 removed outlier: 4.462A pdb=" N GLY B 66 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA B 471 " --> pdb=" O ASN B 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 384 through 385 removed outlier: 6.637A pdb=" N ILE B 384 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE B 688 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 696 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 706 " --> pdb=" O ARG B 697 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 726 through 729 removed outlier: 6.838A pdb=" N LEU B 809 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY B 872 " --> pdb=" O SER B 895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 873 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 848 " --> pdb=" O SER B 873 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 755 through 762 removed outlier: 3.581A pdb=" N VAL B 773 " --> pdb=" O MET B 756 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS B 771 " --> pdb=" O GLU B 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 760 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 769 " --> pdb=" O VAL B 760 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 768 " --> pdb=" O LEU B 787 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 821 through 826 removed outlier: 3.946A pdb=" N GLY B 829 " --> pdb=" O CYS B 826 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 950 through 951 removed outlier: 3.578A pdb=" N ALA B1030 " --> pdb=" O LEU B 989 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 958 through 965 removed outlier: 5.656A pdb=" N LEU B 960 " --> pdb=" O TYR B 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR B 978 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR B1041 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.513A pdb=" N THR C 195 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 62 removed outlier: 4.644A pdb=" N LEU C 33 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 73 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 114 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 124 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 66 through 67 removed outlier: 4.461A pdb=" N GLY C 66 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA C 471 " --> pdb=" O ASN C 268 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 384 through 385 removed outlier: 6.637A pdb=" N ILE C 384 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE C 688 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 696 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 706 " --> pdb=" O ARG C 697 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 726 through 729 removed outlier: 6.839A pdb=" N LEU C 809 " --> pdb=" O LEU C 896 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY C 872 " --> pdb=" O SER C 895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 873 " --> pdb=" O SER C 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 848 " --> pdb=" O SER C 873 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 755 through 762 removed outlier: 3.581A pdb=" N VAL C 773 " --> pdb=" O MET C 756 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS C 771 " --> pdb=" O GLU C 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 760 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA C 769 " --> pdb=" O VAL C 760 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 768 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 821 through 826 removed outlier: 3.945A pdb=" N GLY C 829 " --> pdb=" O CYS C 826 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 950 through 951 removed outlier: 3.579A pdb=" N ALA C1030 " --> pdb=" O LEU C 989 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 958 through 965 removed outlier: 5.656A pdb=" N LEU C 960 " --> pdb=" O TYR C 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR C 978 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C1041 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.512A pdb=" N THR D 195 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 60 through 62 removed outlier: 4.645A pdb=" N LEU D 33 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D 73 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 114 " --> pdb=" O GLU D 157 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 124 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 66 through 67 removed outlier: 4.462A pdb=" N GLY D 66 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 470 through 475 removed outlier: 3.699A pdb=" N ALA D 471 " --> pdb=" O ASN D 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 384 through 385 removed outlier: 6.638A pdb=" N ILE D 384 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 679 through 682 removed outlier: 3.616A pdb=" N ILE D 688 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 696 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 706 " --> pdb=" O ARG D 697 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 726 through 729 removed outlier: 6.838A pdb=" N LEU D 809 " --> pdb=" O LEU D 896 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLY D 872 " --> pdb=" O SER D 895 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 873 " --> pdb=" O SER D 848 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER D 848 " --> pdb=" O SER D 873 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 755 through 762 removed outlier: 3.581A pdb=" N VAL D 773 " --> pdb=" O MET D 756 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N HIS D 771 " --> pdb=" O GLU D 758 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL D 760 " --> pdb=" O ALA D 769 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA D 769 " --> pdb=" O VAL D 760 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 768 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 821 through 826 removed outlier: 3.945A pdb=" N GLY D 829 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 950 through 951 removed outlier: 3.579A pdb=" N ALA D1030 " --> pdb=" O LEU D 989 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 958 through 965 removed outlier: 5.656A pdb=" N LEU D 960 " --> pdb=" O TYR D 978 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR D 978 " --> pdb=" O LEU D 960 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR D1041 " --> pdb=" O VAL D1003 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3540 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: 7.39 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5627 1.32 - 1.44: 9030 1.44 - 1.57: 18507 1.57 - 1.69: 0 1.69 - 1.82: 244 Bond restraints: 33408 Sorted by residual: bond pdb=" C HIS D 276 " pdb=" O HIS D 276 " ideal model delta sigma weight residual 1.235 1.197 0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" C HIS B 276 " pdb=" O HIS B 276 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" C HIS C 276 " pdb=" O HIS C 276 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" CA ALA A 275 " pdb=" CB ALA A 275 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.46e-02 4.69e+03 8.39e+00 bond pdb=" N LEU A 282 " pdb=" CA LEU A 282 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.28e-02 6.10e+03 8.16e+00 ... (remaining 33403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 44185 1.68 - 3.36: 1050 3.36 - 5.04: 168 5.04 - 6.72: 49 6.72 - 8.40: 12 Bond angle restraints: 45464 Sorted by residual: angle pdb=" CA TRP B 283 " pdb=" C TRP B 283 " pdb=" N PRO B 284 " ideal model delta sigma weight residual 118.33 124.48 -6.15 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA TRP C 283 " pdb=" C TRP C 283 " pdb=" N PRO C 284 " ideal model delta sigma weight residual 118.33 124.46 -6.13 1.00e+00 1.00e+00 3.75e+01 angle pdb=" CA TRP D 283 " pdb=" C TRP D 283 " pdb=" N PRO D 284 " ideal model delta sigma weight residual 118.33 124.44 -6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C ASP A 388 " pdb=" CA ASP A 388 " pdb=" CB ASP A 388 " ideal model delta sigma weight residual 111.43 104.73 6.70 1.24e+00 6.50e-01 2.92e+01 angle pdb=" C ASP C 388 " pdb=" CA ASP C 388 " pdb=" CB ASP C 388 " ideal model delta sigma weight residual 111.43 104.92 6.51 1.24e+00 6.50e-01 2.76e+01 ... (remaining 45459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 17207 14.87 - 29.73: 1865 29.73 - 44.60: 710 44.60 - 59.47: 62 59.47 - 74.34: 28 Dihedral angle restraints: 19872 sinusoidal: 7904 harmonic: 11968 Sorted by residual: dihedral pdb=" CA TRP D 739 " pdb=" C TRP D 739 " pdb=" N ASP D 740 " pdb=" CA ASP D 740 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA TRP B 739 " pdb=" C TRP B 739 " pdb=" N ASP B 740 " pdb=" CA ASP B 740 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA TRP C 739 " pdb=" C TRP C 739 " pdb=" N ASP C 740 " pdb=" CA ASP C 740 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 19869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3866 0.047 - 0.093: 786 0.093 - 0.140: 272 0.140 - 0.187: 10 0.187 - 0.233: 14 Chirality restraints: 4948 Sorted by residual: chirality pdb=" CA TRP C 281 " pdb=" N TRP C 281 " pdb=" C TRP C 281 " pdb=" CB TRP C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TRP B 281 " pdb=" N TRP B 281 " pdb=" C TRP B 281 " pdb=" CB TRP B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TRP D 281 " pdb=" N TRP D 281 " pdb=" C TRP D 281 " pdb=" CB TRP D 281 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4945 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 274 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C HIS A 274 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS A 274 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 275 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 476 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C GLY D 476 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY D 476 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE D 477 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 476 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C GLY C 476 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY C 476 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE C 477 " 0.015 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 197 2.55 - 3.14: 24306 3.14 - 3.73: 49530 3.73 - 4.31: 65807 4.31 - 4.90: 114292 Nonbonded interactions: 254132 Sorted by model distance: nonbonded pdb=" OD2 ASP B 278 " pdb="ZN ZN B1101 " model vdw 1.969 2.230 nonbonded pdb=" OD2 ASP C 278 " pdb="ZN ZN C1101 " model vdw 1.990 2.230 nonbonded pdb=" OD2 ASP A 278 " pdb="ZN ZN A1101 " model vdw 2.090 2.230 nonbonded pdb=" OD2 ASP D 278 " pdb="ZN ZN D1101 " model vdw 2.105 2.230 nonbonded pdb=" OD2 ASP D 388 " pdb="ZN ZN D1101 " model vdw 2.128 2.230 ... (remaining 254127 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: 0.08 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.790 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 33416 Z= 0.193 Angle : 0.626 8.397 45464 Z= 0.351 Chirality : 0.044 0.233 4948 Planarity : 0.004 0.038 5996 Dihedral : 13.888 74.335 12168 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.12 % Allowed : 0.32 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4144 helix: 1.92 (0.16), residues: 1100 sheet: -0.13 (0.19), residues: 908 loop : -2.05 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 888 TYR 0.012 0.001 TYR C 204 PHE 0.010 0.001 PHE D 853 TRP 0.014 0.001 TRP D 101 HIS 0.013 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00279 (33408) covalent geometry : angle 0.62628 (45464) hydrogen bonds : bond 0.14611 ( 1256) hydrogen bonds : angle 5.24306 ( 3540) metal coordination : bond 0.19189 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 677 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7822 (ttt) cc_final: 0.7147 (ttm) REVERT: A 313 MET cc_start: 0.8703 (ttm) cc_final: 0.8340 (ttp) REVERT: A 411 GLN cc_start: 0.7345 (pp30) cc_final: 0.7089 (pp30) REVERT: A 1004 ASN cc_start: 0.8931 (p0) cc_final: 0.8723 (p0) REVERT: A 1046 ARG cc_start: 0.7201 (tmm160) cc_final: 0.6530 (ttt90) REVERT: B 192 MET cc_start: 0.7802 (ttt) cc_final: 0.7127 (ttm) REVERT: B 313 MET cc_start: 0.8699 (ttm) cc_final: 0.8344 (ttp) REVERT: B 411 GLN cc_start: 0.7325 (pp30) cc_final: 0.7082 (pp30) REVERT: B 1046 ARG cc_start: 0.7226 (tmm160) cc_final: 0.6542 (ttt90) REVERT: C 192 MET cc_start: 0.7811 (ttt) cc_final: 0.7138 (ttm) REVERT: C 313 MET cc_start: 0.8704 (ttm) cc_final: 0.8345 (ttp) REVERT: C 411 GLN cc_start: 0.7349 (pp30) cc_final: 0.7096 (pp30) REVERT: C 1046 ARG cc_start: 0.7217 (tmm160) cc_final: 0.6531 (ttt90) REVERT: D 192 MET cc_start: 0.7807 (ttt) cc_final: 0.7137 (ttm) REVERT: D 313 MET cc_start: 0.8683 (ttm) cc_final: 0.8334 (ttp) REVERT: D 411 GLN cc_start: 0.7324 (pp30) cc_final: 0.7070 (pp30) REVERT: D 657 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8595 (Cg_endo) outliers start: 4 outliers final: 4 residues processed: 681 average time/residue: 0.1925 time to fit residues: 216.8953 Evaluate side-chains 531 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 527 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain D residue 599 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 149 HIS A 274 HIS A 365 GLN A 424 HIS A 838 ASN B 130 ASN B 149 HIS B 274 HIS B 365 GLN B 424 HIS ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 838 ASN ** B 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 149 HIS C 274 HIS C 365 GLN C 424 HIS ** C 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 ASN ** C 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 149 HIS D 274 HIS D 365 GLN D 424 HIS D 838 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100677 restraints weight = 58595.873| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.17 r_work: 0.3082 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33416 Z= 0.153 Angle : 0.578 7.482 45464 Z= 0.296 Chirality : 0.044 0.156 4948 Planarity : 0.004 0.043 5996 Dihedral : 4.479 47.327 4592 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.55 % Allowed : 10.17 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4144 helix: 1.80 (0.16), residues: 1128 sheet: -0.49 (0.17), residues: 996 loop : -2.07 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 713 TYR 0.013 0.001 TYR B 225 PHE 0.011 0.001 PHE C 853 TRP 0.012 0.001 TRP B 283 HIS 0.005 0.001 HIS A 37 Details of bonding type rmsd covalent geometry : bond 0.00352 (33408) covalent geometry : angle 0.57849 (45464) hydrogen bonds : bond 0.04145 ( 1256) hydrogen bonds : angle 4.56528 ( 3540) metal coordination : bond 0.00479 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 522 time to evaluate : 1.241 Fit side-chains REVERT: A 169 PRO cc_start: 0.8001 (Cg_exo) cc_final: 0.7676 (Cg_endo) REVERT: A 217 GLU cc_start: 0.7974 (pt0) cc_final: 0.7515 (pt0) REVERT: A 411 GLN cc_start: 0.7797 (pp30) cc_final: 0.7258 (pp30) REVERT: A 456 MET cc_start: 0.8455 (mtp) cc_final: 0.8130 (mtp) REVERT: A 780 GLU cc_start: 0.8460 (pp20) cc_final: 0.8227 (pp20) REVERT: B 169 PRO cc_start: 0.8001 (Cg_exo) cc_final: 0.7679 (Cg_endo) REVERT: B 217 GLU cc_start: 0.7970 (pt0) cc_final: 0.7517 (pt0) REVERT: B 411 GLN cc_start: 0.7776 (pp30) cc_final: 0.7250 (pp30) REVERT: B 456 MET cc_start: 0.8482 (mtp) cc_final: 0.8149 (mtp) REVERT: C 169 PRO cc_start: 0.7995 (Cg_exo) cc_final: 0.7673 (Cg_endo) REVERT: C 217 GLU cc_start: 0.7992 (pt0) cc_final: 0.7530 (pt0) REVERT: C 411 GLN cc_start: 0.7803 (pp30) cc_final: 0.7257 (pp30) REVERT: C 456 MET cc_start: 0.8486 (mtp) cc_final: 0.8147 (mtp) REVERT: D 169 PRO cc_start: 0.7965 (Cg_exo) cc_final: 0.7648 (Cg_endo) REVERT: D 217 GLU cc_start: 0.8007 (pt0) cc_final: 0.7537 (pt0) REVERT: D 411 GLN cc_start: 0.7788 (pp30) cc_final: 0.7246 (pp30) REVERT: D 456 MET cc_start: 0.8460 (mtp) cc_final: 0.8127 (mtp) outliers start: 53 outliers final: 37 residues processed: 546 average time/residue: 0.1874 time to fit residues: 171.3409 Evaluate side-chains 513 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 476 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 850 THR Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 850 THR Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 850 THR Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 179 optimal weight: 9.9990 chunk 350 optimal weight: 0.0050 chunk 187 optimal weight: 8.9990 chunk 237 optimal weight: 3.9990 chunk 390 optimal weight: 1.9990 chunk 252 optimal weight: 0.0000 chunk 215 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 735 HIS B 149 HIS B 735 HIS B 827 GLN B 851 HIS C 149 HIS C 735 HIS C 827 GLN C 851 HIS D 149 HIS D 735 HIS D 827 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098345 restraints weight = 58627.501| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.01 r_work: 0.3058 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33416 Z= 0.173 Angle : 0.577 7.070 45464 Z= 0.297 Chirality : 0.045 0.201 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.455 24.076 4584 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.32 % Allowed : 13.63 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4144 helix: 1.76 (0.16), residues: 1128 sheet: -0.50 (0.17), residues: 996 loop : -2.08 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 713 TYR 0.015 0.001 TYR A 225 PHE 0.013 0.001 PHE D 853 TRP 0.012 0.001 TRP C 407 HIS 0.006 0.001 HIS D 735 Details of bonding type rmsd covalent geometry : bond 0.00404 (33408) covalent geometry : angle 0.57727 (45464) hydrogen bonds : bond 0.04153 ( 1256) hydrogen bonds : angle 4.48741 ( 3540) metal coordination : bond 0.00158 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 498 time to evaluate : 1.394 Fit side-chains REVERT: A 16 MET cc_start: 0.8460 (mpp) cc_final: 0.8158 (mpp) REVERT: A 49 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9138 (mm) REVERT: A 169 PRO cc_start: 0.8190 (Cg_exo) cc_final: 0.7888 (Cg_endo) REVERT: A 217 GLU cc_start: 0.8021 (pt0) cc_final: 0.7764 (pt0) REVERT: A 411 GLN cc_start: 0.7843 (pp30) cc_final: 0.7134 (pp30) REVERT: A 456 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8235 (mtp) REVERT: A 707 LEU cc_start: 0.9657 (tt) cc_final: 0.9394 (tt) REVERT: A 740 ASP cc_start: 0.6467 (t0) cc_final: 0.6133 (t0) REVERT: A 742 GLN cc_start: 0.8309 (mp10) cc_final: 0.7925 (mp10) REVERT: B 16 MET cc_start: 0.8468 (mpp) cc_final: 0.8182 (mpp) REVERT: B 49 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9126 (mm) REVERT: B 116 TYR cc_start: 0.9387 (m-80) cc_final: 0.9131 (m-80) REVERT: B 169 PRO cc_start: 0.8182 (Cg_exo) cc_final: 0.7881 (Cg_endo) REVERT: B 217 GLU cc_start: 0.8030 (pt0) cc_final: 0.7797 (pt0) REVERT: B 411 GLN cc_start: 0.7833 (pp30) cc_final: 0.7147 (pp30) REVERT: B 456 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (mtp) REVERT: B 707 LEU cc_start: 0.9656 (tt) cc_final: 0.9390 (tt) REVERT: B 740 ASP cc_start: 0.6462 (t0) cc_final: 0.6136 (t0) REVERT: B 742 GLN cc_start: 0.8314 (mp10) cc_final: 0.7917 (mp10) REVERT: C 16 MET cc_start: 0.8459 (mpp) cc_final: 0.8162 (mpp) REVERT: C 49 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9125 (mm) REVERT: C 116 TYR cc_start: 0.9382 (m-80) cc_final: 0.9125 (m-80) REVERT: C 169 PRO cc_start: 0.8167 (Cg_exo) cc_final: 0.7864 (Cg_endo) REVERT: C 217 GLU cc_start: 0.7992 (pt0) cc_final: 0.7750 (pt0) REVERT: C 411 GLN cc_start: 0.7840 (pp30) cc_final: 0.7137 (pp30) REVERT: C 456 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8263 (mtp) REVERT: C 707 LEU cc_start: 0.9657 (tt) cc_final: 0.9393 (tt) REVERT: C 740 ASP cc_start: 0.6466 (t0) cc_final: 0.6140 (t0) REVERT: C 742 GLN cc_start: 0.8313 (mp10) cc_final: 0.7925 (mp10) REVERT: D 16 MET cc_start: 0.8462 (mpp) cc_final: 0.8161 (mpp) REVERT: D 49 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9136 (mm) REVERT: D 169 PRO cc_start: 0.8169 (Cg_exo) cc_final: 0.7869 (Cg_endo) REVERT: D 217 GLU cc_start: 0.8026 (pt0) cc_final: 0.7792 (pt0) REVERT: D 411 GLN cc_start: 0.7843 (pp30) cc_final: 0.7132 (pp30) REVERT: D 456 MET cc_start: 0.8572 (mtp) cc_final: 0.8276 (mtp) REVERT: D 707 LEU cc_start: 0.9656 (tt) cc_final: 0.9388 (tt) REVERT: D 740 ASP cc_start: 0.6621 (t0) cc_final: 0.6254 (t0) REVERT: D 742 GLN cc_start: 0.8287 (mp10) cc_final: 0.7959 (mp10) outliers start: 79 outliers final: 53 residues processed: 532 average time/residue: 0.1897 time to fit residues: 168.6938 Evaluate side-chains 516 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 456 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 62 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 199 optimal weight: 0.0000 chunk 252 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 838 ASN B 149 HIS B 838 ASN C 149 HIS C 838 ASN D 149 HIS D 838 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097602 restraints weight = 58606.800| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.16 r_work: 0.3051 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33416 Z= 0.151 Angle : 0.558 6.884 45464 Z= 0.287 Chirality : 0.044 0.233 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.442 23.843 4584 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.46 % Allowed : 16.21 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.13), residues: 4144 helix: 1.78 (0.16), residues: 1128 sheet: -0.50 (0.17), residues: 1000 loop : -2.09 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 713 TYR 0.014 0.001 TYR A 225 PHE 0.013 0.001 PHE A 853 TRP 0.012 0.001 TRP C 407 HIS 0.005 0.001 HIS D 598 Details of bonding type rmsd covalent geometry : bond 0.00354 (33408) covalent geometry : angle 0.55828 (45464) hydrogen bonds : bond 0.03920 ( 1256) hydrogen bonds : angle 4.41464 ( 3540) metal coordination : bond 0.00115 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 487 time to evaluate : 1.153 Fit side-chains REVERT: A 16 MET cc_start: 0.8504 (mpp) cc_final: 0.8155 (mpp) REVERT: A 49 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9085 (mm) REVERT: A 116 TYR cc_start: 0.9367 (m-80) cc_final: 0.9053 (m-80) REVERT: A 217 GLU cc_start: 0.7992 (pt0) cc_final: 0.7674 (pt0) REVERT: A 411 GLN cc_start: 0.7875 (pp30) cc_final: 0.7204 (pp30) REVERT: A 456 MET cc_start: 0.8529 (mtp) cc_final: 0.8023 (mtp) REVERT: A 742 GLN cc_start: 0.8377 (mp10) cc_final: 0.8122 (mp10) REVERT: A 939 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8810 (mmt) REVERT: B 16 MET cc_start: 0.8516 (mpp) cc_final: 0.8178 (mpp) REVERT: B 49 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 116 TYR cc_start: 0.9372 (m-80) cc_final: 0.9033 (m-80) REVERT: B 217 GLU cc_start: 0.7983 (pt0) cc_final: 0.7663 (pt0) REVERT: B 411 GLN cc_start: 0.7863 (pp30) cc_final: 0.7198 (pp30) REVERT: B 456 MET cc_start: 0.8546 (mtp) cc_final: 0.8041 (mtp) REVERT: B 742 GLN cc_start: 0.8381 (mp10) cc_final: 0.8122 (mp10) REVERT: C 16 MET cc_start: 0.8521 (mpp) cc_final: 0.8176 (mpp) REVERT: C 49 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9077 (mm) REVERT: C 116 TYR cc_start: 0.9372 (m-80) cc_final: 0.9037 (m-80) REVERT: C 192 MET cc_start: 0.7812 (ttm) cc_final: 0.7608 (ttt) REVERT: C 217 GLU cc_start: 0.7956 (pt0) cc_final: 0.7629 (pt0) REVERT: C 411 GLN cc_start: 0.7873 (pp30) cc_final: 0.7194 (pp30) REVERT: C 456 MET cc_start: 0.8534 (mtp) cc_final: 0.8018 (mtp) REVERT: C 742 GLN cc_start: 0.8376 (mp10) cc_final: 0.8109 (mp10) REVERT: D 16 MET cc_start: 0.8520 (mpp) cc_final: 0.8180 (mpp) REVERT: D 49 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9082 (mm) REVERT: D 192 MET cc_start: 0.7820 (ttm) cc_final: 0.7619 (ttt) REVERT: D 217 GLU cc_start: 0.7990 (pt0) cc_final: 0.7627 (pt0) REVERT: D 411 GLN cc_start: 0.7883 (pp30) cc_final: 0.7199 (pp30) REVERT: D 456 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7997 (mtp) REVERT: D 740 ASP cc_start: 0.6721 (t0) cc_final: 0.6369 (t0) REVERT: D 742 GLN cc_start: 0.8291 (mp10) cc_final: 0.7805 (mp10) REVERT: D 939 MET cc_start: 0.8933 (mmm) cc_final: 0.8645 (mmt) outliers start: 84 outliers final: 66 residues processed: 533 average time/residue: 0.1963 time to fit residues: 173.8598 Evaluate side-chains 508 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 436 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 696 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 8 optimal weight: 9.9990 chunk 366 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 367 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 167 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094627 restraints weight = 59740.223| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.09 r_work: 0.2994 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 33416 Z= 0.238 Angle : 0.635 9.733 45464 Z= 0.327 Chirality : 0.046 0.260 4948 Planarity : 0.004 0.046 5996 Dihedral : 4.748 24.878 4584 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.63 % Allowed : 16.35 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4144 helix: 1.69 (0.16), residues: 1128 sheet: -0.35 (0.17), residues: 956 loop : -2.28 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 840 TYR 0.018 0.001 TYR D 225 PHE 0.015 0.002 PHE A 853 TRP 0.014 0.002 TRP D 396 HIS 0.005 0.001 HIS B 598 Details of bonding type rmsd covalent geometry : bond 0.00552 (33408) covalent geometry : angle 0.63468 (45464) hydrogen bonds : bond 0.04586 ( 1256) hydrogen bonds : angle 4.61443 ( 3540) metal coordination : bond 0.00166 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 456 time to evaluate : 1.178 Fit side-chains REVERT: A 16 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8318 (mpp) REVERT: A 217 GLU cc_start: 0.7988 (pt0) cc_final: 0.7679 (pt0) REVERT: A 305 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: A 411 GLN cc_start: 0.8081 (pp30) cc_final: 0.7371 (pp30) REVERT: A 456 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7937 (mtp) REVERT: A 740 ASP cc_start: 0.6651 (t0) cc_final: 0.6137 (t0) REVERT: A 742 GLN cc_start: 0.8277 (mp10) cc_final: 0.7851 (mp10) REVERT: B 16 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8321 (mpp) REVERT: B 49 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9158 (mm) REVERT: B 217 GLU cc_start: 0.7959 (pt0) cc_final: 0.7639 (pt0) REVERT: B 305 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: B 411 GLN cc_start: 0.8076 (pp30) cc_final: 0.7373 (pp30) REVERT: B 456 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7939 (mtp) REVERT: B 740 ASP cc_start: 0.6641 (t0) cc_final: 0.6135 (t0) REVERT: B 742 GLN cc_start: 0.8279 (mp10) cc_final: 0.7871 (mp10) REVERT: B 939 MET cc_start: 0.8963 (mmm) cc_final: 0.8624 (mmt) REVERT: C 16 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8306 (mpp) REVERT: C 49 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9157 (mm) REVERT: C 217 GLU cc_start: 0.7954 (pt0) cc_final: 0.7651 (pt0) REVERT: C 305 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (pp20) REVERT: C 411 GLN cc_start: 0.8065 (pp30) cc_final: 0.7339 (pp30) REVERT: C 456 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7964 (mtp) REVERT: C 740 ASP cc_start: 0.6651 (t0) cc_final: 0.6141 (t0) REVERT: C 742 GLN cc_start: 0.8269 (mp10) cc_final: 0.7863 (mp10) REVERT: C 939 MET cc_start: 0.8960 (mmm) cc_final: 0.8622 (mmt) REVERT: D 16 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8292 (mpp) REVERT: D 217 GLU cc_start: 0.7966 (pt0) cc_final: 0.7638 (pt0) REVERT: D 305 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8318 (pp20) REVERT: D 411 GLN cc_start: 0.8083 (pp30) cc_final: 0.7356 (pp30) REVERT: D 456 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7960 (mtp) REVERT: D 740 ASP cc_start: 0.6790 (t0) cc_final: 0.6563 (t0) REVERT: D 742 GLN cc_start: 0.8220 (mp10) cc_final: 0.7881 (mp10) outliers start: 124 outliers final: 85 residues processed: 528 average time/residue: 0.1832 time to fit residues: 161.7286 Evaluate side-chains 532 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 433 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 218 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 403 optimal weight: 5.9990 chunk 339 optimal weight: 0.7980 chunk 170 optimal weight: 0.2980 chunk 312 optimal weight: 2.9990 chunk 381 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN B 149 HIS B 838 ASN C 149 HIS C 838 ASN D 149 HIS D 838 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096991 restraints weight = 58770.590| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.14 r_work: 0.3032 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33416 Z= 0.145 Angle : 0.593 11.289 45464 Z= 0.299 Chirality : 0.044 0.161 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.598 24.590 4584 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.17 % Allowed : 18.05 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4144 helix: 1.76 (0.16), residues: 1128 sheet: -0.28 (0.18), residues: 940 loop : -2.21 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 713 TYR 0.014 0.001 TYR B 225 PHE 0.014 0.001 PHE D 853 TRP 0.014 0.001 TRP C 407 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00341 (33408) covalent geometry : angle 0.59326 (45464) hydrogen bonds : bond 0.03894 ( 1256) hydrogen bonds : angle 4.40395 ( 3540) metal coordination : bond 0.00105 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 486 time to evaluate : 1.225 Fit side-chains REVERT: A 116 TYR cc_start: 0.9378 (m-80) cc_final: 0.9106 (m-80) REVERT: A 217 GLU cc_start: 0.7940 (pt0) cc_final: 0.7677 (pt0) REVERT: A 411 GLN cc_start: 0.8042 (pp30) cc_final: 0.7465 (pp30) REVERT: A 456 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7897 (mtp) REVERT: A 584 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: A 742 GLN cc_start: 0.8296 (mp10) cc_final: 0.7999 (mp10) REVERT: A 1002 GLU cc_start: 0.8387 (pm20) cc_final: 0.8115 (pm20) REVERT: B 49 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9074 (mm) REVERT: B 116 TYR cc_start: 0.9382 (m-80) cc_final: 0.9101 (m-80) REVERT: B 217 GLU cc_start: 0.7934 (pt0) cc_final: 0.7669 (pt0) REVERT: B 411 GLN cc_start: 0.8041 (pp30) cc_final: 0.7483 (pp30) REVERT: B 456 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7887 (mtp) REVERT: B 584 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: B 742 GLN cc_start: 0.8267 (mp10) cc_final: 0.7965 (mp10) REVERT: B 1002 GLU cc_start: 0.8405 (pm20) cc_final: 0.8117 (pm20) REVERT: C 16 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8284 (mpp) REVERT: C 49 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9070 (mm) REVERT: C 116 TYR cc_start: 0.9373 (m-80) cc_final: 0.9086 (m-80) REVERT: C 217 GLU cc_start: 0.7914 (pt0) cc_final: 0.7661 (pt0) REVERT: C 411 GLN cc_start: 0.8032 (pp30) cc_final: 0.7462 (pp30) REVERT: C 456 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7890 (mtp) REVERT: C 584 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: C 742 GLN cc_start: 0.8261 (mp10) cc_final: 0.7958 (mp10) REVERT: C 1002 GLU cc_start: 0.8431 (pm20) cc_final: 0.8149 (pm20) REVERT: D 16 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8284 (mpp) REVERT: D 116 TYR cc_start: 0.9397 (m-80) cc_final: 0.9092 (m-80) REVERT: D 217 GLU cc_start: 0.7921 (pt0) cc_final: 0.7641 (pt0) REVERT: D 411 GLN cc_start: 0.8055 (pp30) cc_final: 0.7479 (pp30) REVERT: D 456 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: D 584 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: D 740 ASP cc_start: 0.6781 (t0) cc_final: 0.6573 (t0) REVERT: D 742 GLN cc_start: 0.8240 (mp10) cc_final: 0.7864 (mp10) REVERT: D 1002 GLU cc_start: 0.8401 (pm20) cc_final: 0.8117 (pm20) outliers start: 108 outliers final: 81 residues processed: 550 average time/residue: 0.1951 time to fit residues: 177.0381 Evaluate side-chains 535 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 442 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 838 ASN Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 696 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 838 ASN Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 838 ASN Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 105 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 336 optimal weight: 0.0070 chunk 58 optimal weight: 0.7980 chunk 398 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094311 restraints weight = 59377.435| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.04 r_work: 0.2992 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 33416 Z= 0.226 Angle : 0.639 10.008 45464 Z= 0.326 Chirality : 0.046 0.310 4948 Planarity : 0.004 0.046 5996 Dihedral : 4.747 25.121 4584 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.34 % Allowed : 18.49 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4144 helix: 1.64 (0.16), residues: 1128 sheet: -0.41 (0.17), residues: 956 loop : -2.36 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 713 TYR 0.017 0.001 TYR B 225 PHE 0.016 0.002 PHE A 853 TRP 0.014 0.002 TRP A 407 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00527 (33408) covalent geometry : angle 0.63915 (45464) hydrogen bonds : bond 0.04406 ( 1256) hydrogen bonds : angle 4.55114 ( 3540) metal coordination : bond 0.00152 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 450 time to evaluate : 1.281 Fit side-chains REVERT: A 16 MET cc_start: 0.8440 (mpp) cc_final: 0.7891 (mpp) REVERT: A 116 TYR cc_start: 0.9377 (m-80) cc_final: 0.9124 (m-80) REVERT: A 217 GLU cc_start: 0.7941 (pt0) cc_final: 0.7660 (pt0) REVERT: A 411 GLN cc_start: 0.8114 (pp30) cc_final: 0.7575 (pp30) REVERT: A 456 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: A 584 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: A 953 ASP cc_start: 0.8964 (m-30) cc_final: 0.8722 (m-30) REVERT: A 1002 GLU cc_start: 0.8464 (pm20) cc_final: 0.8202 (pm20) REVERT: B 16 MET cc_start: 0.8436 (mpp) cc_final: 0.7858 (mpp) REVERT: B 49 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9148 (mm) REVERT: B 116 TYR cc_start: 0.9384 (m-80) cc_final: 0.9126 (m-80) REVERT: B 217 GLU cc_start: 0.7943 (pt0) cc_final: 0.7653 (pt0) REVERT: B 411 GLN cc_start: 0.8114 (pp30) cc_final: 0.7571 (pp30) REVERT: B 456 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7853 (mtp) REVERT: B 584 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: B 939 MET cc_start: 0.8977 (mmm) cc_final: 0.8658 (mmt) REVERT: B 953 ASP cc_start: 0.8969 (m-30) cc_final: 0.8733 (m-30) REVERT: B 1002 GLU cc_start: 0.8461 (pm20) cc_final: 0.8187 (pm20) REVERT: C 16 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8326 (mpp) REVERT: C 49 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9143 (mm) REVERT: C 116 TYR cc_start: 0.9378 (m-80) cc_final: 0.9122 (m-80) REVERT: C 217 GLU cc_start: 0.7936 (pt0) cc_final: 0.7664 (pt0) REVERT: C 411 GLN cc_start: 0.8116 (pp30) cc_final: 0.7582 (pp30) REVERT: C 456 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.7892 (mtp) REVERT: C 584 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: C 939 MET cc_start: 0.8973 (mmm) cc_final: 0.8660 (mmt) REVERT: C 953 ASP cc_start: 0.8969 (m-30) cc_final: 0.8730 (m-30) REVERT: C 1002 GLU cc_start: 0.8471 (pm20) cc_final: 0.8197 (pm20) REVERT: D 16 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8317 (mpp) REVERT: D 116 TYR cc_start: 0.9397 (m-80) cc_final: 0.9121 (m-80) REVERT: D 217 GLU cc_start: 0.7930 (pt0) cc_final: 0.7644 (pt0) REVERT: D 411 GLN cc_start: 0.8114 (pp30) cc_final: 0.7582 (pp30) REVERT: D 456 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7897 (mtp) REVERT: D 584 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: D 742 GLN cc_start: 0.8231 (mp10) cc_final: 0.7911 (mp10) REVERT: D 939 MET cc_start: 0.8831 (mmm) cc_final: 0.8534 (mmp) REVERT: D 953 ASP cc_start: 0.8957 (m-30) cc_final: 0.8713 (m-30) REVERT: D 1002 GLU cc_start: 0.8488 (pm20) cc_final: 0.8215 (pm20) outliers start: 148 outliers final: 98 residues processed: 536 average time/residue: 0.1870 time to fit residues: 167.1915 Evaluate side-chains 543 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 433 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 16 MET Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1020 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 438 THR Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 784 VAL Chi-restraints excluded: chain D residue 801 ASN Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 820 VAL Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 205 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 73 optimal weight: 0.0020 chunk 288 optimal weight: 0.9990 chunk 309 optimal weight: 0.3980 chunk 352 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 376 HIS B 149 HIS B 376 HIS C 149 HIS C 376 HIS D 149 HIS D 376 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099955 restraints weight = 58740.013| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.05 r_work: 0.3078 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33416 Z= 0.106 Angle : 0.581 9.033 45464 Z= 0.293 Chirality : 0.043 0.208 4948 Planarity : 0.004 0.044 5996 Dihedral : 4.473 24.846 4584 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.43 % Allowed : 20.34 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4144 helix: 1.72 (0.16), residues: 1140 sheet: -0.10 (0.18), residues: 908 loop : -2.27 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 713 TYR 0.012 0.001 TYR D 225 PHE 0.014 0.001 PHE D 853 TRP 0.014 0.001 TRP B 407 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00246 (33408) covalent geometry : angle 0.58134 (45464) hydrogen bonds : bond 0.03406 ( 1256) hydrogen bonds : angle 4.24924 ( 3540) metal coordination : bond 0.00077 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 534 time to evaluate : 1.301 Fit side-chains REVERT: A 7 GLN cc_start: 0.7942 (tt0) cc_final: 0.7461 (mm110) REVERT: A 16 MET cc_start: 0.8304 (mpp) cc_final: 0.7788 (mpp) REVERT: A 116 TYR cc_start: 0.9361 (m-80) cc_final: 0.9059 (m-80) REVERT: A 217 GLU cc_start: 0.7850 (pt0) cc_final: 0.7629 (pt0) REVERT: A 411 GLN cc_start: 0.7962 (pp30) cc_final: 0.7389 (pp30) REVERT: A 456 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7793 (mtp) REVERT: A 584 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: A 742 GLN cc_start: 0.7853 (mp10) cc_final: 0.7436 (mp10) REVERT: B 7 GLN cc_start: 0.7915 (tt0) cc_final: 0.7408 (mm110) REVERT: B 16 MET cc_start: 0.8304 (mpp) cc_final: 0.7800 (mpp) REVERT: B 49 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8947 (mm) REVERT: B 116 TYR cc_start: 0.9362 (m-80) cc_final: 0.9053 (m-80) REVERT: B 217 GLU cc_start: 0.7877 (pt0) cc_final: 0.7650 (pt0) REVERT: B 411 GLN cc_start: 0.7937 (pp30) cc_final: 0.7387 (pp30) REVERT: B 456 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7770 (mtp) REVERT: B 584 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: B 742 GLN cc_start: 0.7832 (mp10) cc_final: 0.7413 (mp10) REVERT: C 7 GLN cc_start: 0.7936 (tt0) cc_final: 0.7364 (mm110) REVERT: C 49 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8948 (mm) REVERT: C 116 TYR cc_start: 0.9359 (m-80) cc_final: 0.9044 (m-80) REVERT: C 217 GLU cc_start: 0.7824 (pt0) cc_final: 0.7582 (pt0) REVERT: C 411 GLN cc_start: 0.7956 (pp30) cc_final: 0.7387 (pp30) REVERT: C 456 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7802 (mtp) REVERT: C 584 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: C 742 GLN cc_start: 0.7843 (mp10) cc_final: 0.7350 (mp10) REVERT: D 7 GLN cc_start: 0.7893 (tt0) cc_final: 0.7351 (mm110) REVERT: D 217 GLU cc_start: 0.7862 (pt0) cc_final: 0.7622 (pt0) REVERT: D 411 GLN cc_start: 0.7952 (pp30) cc_final: 0.7392 (pp30) REVERT: D 456 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7829 (mtp) REVERT: D 584 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8521 (mp0) outliers start: 83 outliers final: 59 residues processed: 583 average time/residue: 0.1896 time to fit residues: 184.4461 Evaluate side-chains 540 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 471 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1020 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1020 VAL Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1020 VAL Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 584 GLU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 825 GLU Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1020 VAL Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 58 optimal weight: 0.2980 chunk 294 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 394 optimal weight: 0.9980 chunk 357 optimal weight: 0.2980 chunk 333 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 610 HIS B 149 HIS B 610 HIS C 149 HIS C 610 HIS D 149 HIS D 610 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.116655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099817 restraints weight = 58092.945| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.03 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33416 Z= 0.111 Angle : 0.593 8.483 45464 Z= 0.296 Chirality : 0.043 0.266 4948 Planarity : 0.004 0.043 5996 Dihedral : 4.401 24.114 4584 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.67 % Allowed : 20.84 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.13), residues: 4144 helix: 1.83 (0.16), residues: 1120 sheet: -0.37 (0.17), residues: 976 loop : -2.29 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 713 TYR 0.024 0.001 TYR D 204 PHE 0.014 0.001 PHE D 853 TRP 0.013 0.001 TRP A 739 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00260 (33408) covalent geometry : angle 0.59259 (45464) hydrogen bonds : bond 0.03399 ( 1256) hydrogen bonds : angle 4.21078 ( 3540) metal coordination : bond 0.00047 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 515 time to evaluate : 1.162 Fit side-chains REVERT: A 7 GLN cc_start: 0.7924 (tt0) cc_final: 0.7528 (mm110) REVERT: A 16 MET cc_start: 0.8302 (mpp) cc_final: 0.7797 (mpp) REVERT: A 78 GLU cc_start: 0.7505 (pp20) cc_final: 0.6922 (pp20) REVERT: A 116 TYR cc_start: 0.9346 (m-80) cc_final: 0.9017 (m-80) REVERT: A 192 MET cc_start: 0.7685 (ttm) cc_final: 0.7428 (ttt) REVERT: A 217 GLU cc_start: 0.7810 (pt0) cc_final: 0.7584 (pt0) REVERT: A 411 GLN cc_start: 0.7980 (pp30) cc_final: 0.7399 (pp30) REVERT: A 456 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: B 7 GLN cc_start: 0.7944 (tt0) cc_final: 0.7462 (mm110) REVERT: B 16 MET cc_start: 0.8354 (mpp) cc_final: 0.7819 (mpp) REVERT: B 49 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8954 (mm) REVERT: B 78 GLU cc_start: 0.7504 (pp20) cc_final: 0.6918 (pp20) REVERT: B 192 MET cc_start: 0.7702 (ttm) cc_final: 0.7450 (ttt) REVERT: B 217 GLU cc_start: 0.7821 (pt0) cc_final: 0.7582 (pt0) REVERT: B 411 GLN cc_start: 0.7966 (pp30) cc_final: 0.7395 (pp30) REVERT: B 456 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7777 (mtp) REVERT: B 488 MET cc_start: 0.9119 (ptp) cc_final: 0.8850 (mtm) REVERT: B 939 MET cc_start: 0.8683 (mmm) cc_final: 0.8450 (mmp) REVERT: C 7 GLN cc_start: 0.7940 (tt0) cc_final: 0.7485 (mm110) REVERT: C 16 MET cc_start: 0.8254 (mpp) cc_final: 0.7780 (mpp) REVERT: C 49 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8957 (mm) REVERT: C 78 GLU cc_start: 0.7533 (pp20) cc_final: 0.6953 (pp20) REVERT: C 217 GLU cc_start: 0.7814 (pt0) cc_final: 0.7555 (pt0) REVERT: C 411 GLN cc_start: 0.7973 (pp30) cc_final: 0.7394 (pp30) REVERT: C 456 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7803 (mtp) REVERT: C 488 MET cc_start: 0.9131 (ptp) cc_final: 0.8875 (mtm) REVERT: C 939 MET cc_start: 0.8685 (mmm) cc_final: 0.8449 (mmp) REVERT: D 7 GLN cc_start: 0.7932 (tt0) cc_final: 0.7477 (mm110) REVERT: D 16 MET cc_start: 0.8246 (mpp) cc_final: 0.7795 (mpp) REVERT: D 78 GLU cc_start: 0.7542 (pp20) cc_final: 0.6953 (pp20) REVERT: D 217 GLU cc_start: 0.7826 (pt0) cc_final: 0.7575 (pt0) REVERT: D 411 GLN cc_start: 0.7968 (pp30) cc_final: 0.7393 (pp30) REVERT: D 456 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7831 (mtp) REVERT: D 488 MET cc_start: 0.9135 (ptp) cc_final: 0.8873 (mtm) REVERT: D 742 GLN cc_start: 0.7878 (mp10) cc_final: 0.7164 (tp40) outliers start: 91 outliers final: 67 residues processed: 571 average time/residue: 0.1881 time to fit residues: 178.4162 Evaluate side-chains 560 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 487 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 825 GLU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 991 LEU Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 236 optimal weight: 0.9980 chunk 412 optimal weight: 9.9990 chunk 366 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 299 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS B 149 HIS C 149 HIS D 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094595 restraints weight = 59190.756| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.10 r_work: 0.2899 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33416 Z= 0.187 Angle : 0.632 8.248 45464 Z= 0.320 Chirality : 0.045 0.270 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.584 25.148 4584 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.49 % Allowed : 20.81 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.13), residues: 4144 helix: 1.84 (0.16), residues: 1116 sheet: -0.31 (0.18), residues: 944 loop : -2.33 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 713 TYR 0.015 0.001 TYR D 225 PHE 0.016 0.001 PHE A 163 TRP 0.014 0.001 TRP D 396 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00439 (33408) covalent geometry : angle 0.63250 (45464) hydrogen bonds : bond 0.04014 ( 1256) hydrogen bonds : angle 4.35667 ( 3540) metal coordination : bond 0.00079 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8288 Ramachandran restraints generated. 4144 Oldfield, 0 Emsley, 4144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 457 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7969 (tt0) cc_final: 0.7381 (mm110) REVERT: A 16 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7797 (mpp) REVERT: A 78 GLU cc_start: 0.7487 (pp20) cc_final: 0.6874 (pp20) REVERT: A 217 GLU cc_start: 0.7866 (pt0) cc_final: 0.7613 (pt0) REVERT: A 411 GLN cc_start: 0.8171 (pp30) cc_final: 0.7539 (pp30) REVERT: A 456 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7799 (mtp) REVERT: A 740 ASP cc_start: 0.6659 (t0) cc_final: 0.6363 (t0) REVERT: A 953 ASP cc_start: 0.9034 (m-30) cc_final: 0.8816 (m-30) REVERT: B 7 GLN cc_start: 0.7973 (tt0) cc_final: 0.7480 (mm110) REVERT: B 16 MET cc_start: 0.8372 (mpp) cc_final: 0.7769 (mpp) REVERT: B 49 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8982 (mm) REVERT: B 78 GLU cc_start: 0.7486 (pp20) cc_final: 0.6876 (pp20) REVERT: B 411 GLN cc_start: 0.8171 (pp30) cc_final: 0.7552 (pp30) REVERT: B 740 ASP cc_start: 0.6667 (t0) cc_final: 0.6377 (t0) REVERT: B 939 MET cc_start: 0.8737 (mmm) cc_final: 0.8450 (mmp) REVERT: B 953 ASP cc_start: 0.9034 (m-30) cc_final: 0.8814 (m-30) REVERT: C 7 GLN cc_start: 0.7985 (tt0) cc_final: 0.7484 (mm110) REVERT: C 16 MET cc_start: 0.8301 (mpp) cc_final: 0.7776 (mpp) REVERT: C 49 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8997 (mm) REVERT: C 78 GLU cc_start: 0.7491 (pp20) cc_final: 0.6892 (pp20) REVERT: C 217 GLU cc_start: 0.7863 (pt0) cc_final: 0.7594 (pt0) REVERT: C 411 GLN cc_start: 0.8177 (pp30) cc_final: 0.7546 (pp30) REVERT: C 456 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7843 (mtp) REVERT: C 939 MET cc_start: 0.8744 (mmm) cc_final: 0.8460 (mmp) REVERT: C 953 ASP cc_start: 0.9036 (m-30) cc_final: 0.8816 (m-30) REVERT: D 7 GLN cc_start: 0.7974 (tt0) cc_final: 0.7483 (mm110) REVERT: D 16 MET cc_start: 0.8305 (mpp) cc_final: 0.7778 (mpp) REVERT: D 78 GLU cc_start: 0.7517 (pp20) cc_final: 0.6913 (pp20) REVERT: D 411 GLN cc_start: 0.8173 (pp30) cc_final: 0.7539 (pp30) REVERT: D 742 GLN cc_start: 0.7737 (mp10) cc_final: 0.7206 (mp10) REVERT: D 953 ASP cc_start: 0.9039 (m-30) cc_final: 0.8817 (m-30) outliers start: 85 outliers final: 73 residues processed: 508 average time/residue: 0.1914 time to fit residues: 161.4662 Evaluate side-chains 525 residues out of total 3416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 447 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 101 TRP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1041 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 811 VAL Chi-restraints excluded: chain B residue 820 VAL Chi-restraints excluded: chain B residue 825 GLU Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 870 THR Chi-restraints excluded: chain B residue 952 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1041 THR Chi-restraints excluded: chain C residue 12 CYS Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 101 TRP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 599 ASP Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 811 VAL Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 825 GLU Chi-restraints excluded: chain C residue 848 SER Chi-restraints excluded: chain C residue 870 THR Chi-restraints excluded: chain C residue 952 THR Chi-restraints excluded: chain C residue 959 VAL Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1041 THR Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain D residue 101 TRP Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 599 ASP Chi-restraints excluded: chain D residue 608 TRP Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 680 VAL Chi-restraints excluded: chain D residue 811 VAL Chi-restraints excluded: chain D residue 848 SER Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 959 VAL Chi-restraints excluded: chain D residue 1005 LEU Chi-restraints excluded: chain D residue 1040 VAL Chi-restraints excluded: chain D residue 1041 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 343 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 344 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 270 optimal weight: 0.8980 chunk 333 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 838 ASN B 149 HIS B 838 ASN C 149 HIS C 838 ASN D 149 HIS D 827 GLN D 851 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096308 restraints weight = 58709.167| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.09 r_work: 0.3013 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33416 Z= 0.135 Angle : 0.607 8.232 45464 Z= 0.305 Chirality : 0.044 0.242 4948 Planarity : 0.004 0.045 5996 Dihedral : 4.522 25.092 4584 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.61 % Allowed : 21.31 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4144 helix: 1.82 (0.16), residues: 1116 sheet: -0.26 (0.18), residues: 948 loop : -2.33 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 713 TYR 0.013 0.001 TYR D 225 PHE 0.014 0.001 PHE D 853 TRP 0.014 0.001 TRP D 407 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00320 (33408) covalent geometry : angle 0.60733 (45464) hydrogen bonds : bond 0.03679 ( 1256) hydrogen bonds : angle 4.26553 ( 3540) metal coordination : bond 0.00073 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6339.30 seconds wall clock time: 109 minutes 50.39 seconds (6590.39 seconds total)