Starting phenix.real_space_refine on Wed Mar 4 06:44:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d14_30543/03_2026/7d14_30543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d14_30543/03_2026/7d14_30543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d14_30543/03_2026/7d14_30543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d14_30543/03_2026/7d14_30543.map" model { file = "/net/cci-nas-00/data/ceres_data/7d14_30543/03_2026/7d14_30543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d14_30543/03_2026/7d14_30543_neut.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 7462 2.51 5 N 2010 2.21 5 O 2080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s 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: 11636 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 5818 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 30, 'TRANS': 819} Chain breaks: 11 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 822 Unresolved non-hydrogen angles: 1044 Unresolved non-hydrogen dihedrals: 687 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'ARG:plan': 17, 'PHE:plan': 9, 'GLU:plan': 24, 'ASN:plan1': 12, 'TYR:plan': 10, 'ASP:plan': 15, 'HIS:plan': 9, 'TRP:plan': 2, 'GLN:plan1': 11} Unresolved non-hydrogen planarities: 493 Restraints were copied for chains: B Time building chain proxies: 4.59, per 1000 atoms: 0.39 Number of scatterers: 11636 At special positions: 0 Unit cell: (118.919, 103.645, 147.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2080 8.00 N 2010 7.00 C 7462 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: 0.76 Conformation dependent library (CDL) restraints added in 576.2 milliseconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3100 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 50.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 98 through 107 removed outlier: 4.060A pdb=" N ALA A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.805A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.796A pdb=" N ASN A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 151 through 177 removed outlier: 4.233A pdb=" N CYS A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 169 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 221 removed outlier: 3.954A pdb=" N MET A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.609A pdb=" N GLY A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 247 through 270 removed outlier: 3.569A pdb=" N ASN A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 268 " --> pdb=" O MET A 264 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.068A pdb=" N VAL A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.609A pdb=" N VAL A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER A 289 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.906A pdb=" N GLY A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.607A pdb=" N SER A 441 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 476 removed outlier: 4.197A pdb=" N THR A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 539 removed outlier: 4.747A pdb=" N PHE A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Proline residue: A 530 - end of helix removed outlier: 3.904A pdb=" N ASP A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 removed outlier: 3.938A pdb=" N GLY A 549 " --> pdb=" O GLN A 546 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 550 " --> pdb=" O VAL A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 546 through 550' Processing helix chain 'A' and resid 558 through 573 removed outlier: 4.199A pdb=" N GLY A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 605 removed outlier: 3.691A pdb=" N ALA A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 4.202A pdb=" N MET A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 595 " --> pdb=" O CYS A 591 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 596 " --> pdb=" O TYR A 592 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 603 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 637 removed outlier: 3.730A pdb=" N CYS A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 637 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 661 removed outlier: 4.167A pdb=" N VAL A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 656 " --> pdb=" O TYR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 682 removed outlier: 4.048A pdb=" N SER A 672 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 removed outlier: 4.175A pdb=" N LEU A 715 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 720 " --> pdb=" O SER A 716 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 722 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 759 Proline residue: A 743 - end of helix removed outlier: 3.662A pdb=" N GLU A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 758 " --> pdb=" O ARG A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 859 through 869 removed outlier: 3.593A pdb=" N LEU A 864 " --> pdb=" O MET A 860 " (cutoff:3.500A) Proline residue: A 865 - end of helix Processing helix chain 'A' and resid 893 through 905 Processing helix chain 'A' and resid 927 through 937 removed outlier: 3.700A pdb=" N GLU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1113 removed outlier: 3.532A pdb=" N PHE A1112 " --> pdb=" O ASN A1108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1113 " --> pdb=" O TYR A1109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1108 through 1113' Processing helix chain 'B' and resid 98 through 107 removed outlier: 4.060A pdb=" N ALA B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 133 removed outlier: 3.806A pdb=" N LEU B 128 " --> pdb=" O MET B 124 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.795A pdb=" N ASN B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 151 through 177 removed outlier: 4.233A pdb=" N CYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR B 169 " --> pdb=" O CYS B 165 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 221 removed outlier: 3.954A pdb=" N MET B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Proline residue: B 197 - end of helix removed outlier: 3.608A pdb=" N GLY B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 247 through 270 removed outlier: 3.569A pdb=" N ASN B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 278 removed outlier: 4.068A pdb=" N VAL B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.609A pdb=" N VAL B 286 " --> pdb=" O PHE B 282 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 289 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 431 removed outlier: 3.906A pdb=" N GLY B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 437 through 441 removed outlier: 3.607A pdb=" N SER B 441 " --> pdb=" O MET B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 458 through 476 removed outlier: 4.197A pdb=" N THR B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 539 removed outlier: 4.747A pdb=" N PHE B 515 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 517 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 526 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) Proline residue: B 530 - end of helix removed outlier: 3.904A pdb=" N ASP B 539 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 3.938A pdb=" N GLY B 549 " --> pdb=" O GLN B 546 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B 550 " --> pdb=" O VAL B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 550' Processing helix chain 'B' and resid 558 through 573 removed outlier: 4.198A pdb=" N GLY B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 605 removed outlier: 3.690A pdb=" N ALA B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Proline residue: B 582 - end of helix removed outlier: 4.201A pdb=" N MET B 586 " --> pdb=" O PRO B 582 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 595 " --> pdb=" O CYS B 591 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 596 " --> pdb=" O TYR B 592 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR B 603 " --> pdb=" O CYS B 599 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 604 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 637 removed outlier: 3.730A pdb=" N CYS B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 637 " --> pdb=" O MET B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 661 removed outlier: 4.167A pdb=" N VAL B 643 " --> pdb=" O TYR B 639 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 653 " --> pdb=" O GLY B 649 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 656 " --> pdb=" O TYR B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 removed outlier: 4.047A pdb=" N SER B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 723 removed outlier: 4.175A pdb=" N LEU B 715 " --> pdb=" O HIS B 711 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 720 " --> pdb=" O SER B 716 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 759 Proline residue: B 743 - end of helix removed outlier: 3.662A pdb=" N GLU B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 758 " --> pdb=" O ARG B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 859 through 869 removed outlier: 3.593A pdb=" N LEU B 864 " --> pdb=" O MET B 860 " (cutoff:3.500A) Proline residue: B 865 - end of helix Processing helix chain 'B' and resid 893 through 905 Processing helix chain 'B' and resid 927 through 937 removed outlier: 3.700A pdb=" N GLU B 933 " --> pdb=" O THR B 929 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1113 removed outlier: 3.533A pdb=" N PHE B1112 " --> pdb=" O ASN B1108 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1113 " --> pdb=" O TYR B1109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1108 through 1113' Processing sheet with id=AA1, first strand: chain 'A' and resid 764 through 768 removed outlier: 3.606A pdb=" N VAL A 768 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 697 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY A 731 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 699 " --> pdb=" O GLY A 731 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL A 733 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 698 " --> pdb=" O LEU A 795 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY A 797 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU A 700 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 794 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR A 831 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 796 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1092 " --> pdb=" O MET A1124 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A1126 " --> pdb=" O VAL A1092 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A1094 " --> pdb=" O VAL A1126 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A1095 " --> pdb=" O TRP A 852 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 764 through 768 removed outlier: 3.605A pdb=" N VAL B 768 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 697 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY B 731 " --> pdb=" O LEU B 697 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 699 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL B 733 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 698 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLY B 797 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 700 " --> pdb=" O GLY B 797 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 794 " --> pdb=" O LEU B 829 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR B 831 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 796 " --> pdb=" O THR B 831 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B1092 " --> pdb=" O MET B1124 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL B1126 " --> pdb=" O VAL B1092 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU B1094 " --> pdb=" O VAL B1126 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B1095 " --> pdb=" O TRP B 852 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1524 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: 1.85 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3723 1.34 - 1.46: 1805 1.46 - 1.57: 6164 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 11824 Sorted by residual: bond pdb=" C ILE B 454 " pdb=" N PRO B 455 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.43e+00 bond pdb=" C ILE A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.37e+00 bond pdb=" CA VAL B 913 " pdb=" CB VAL B 913 " ideal model delta sigma weight residual 1.541 1.519 0.023 1.28e-02 6.10e+03 3.15e+00 bond pdb=" CA VAL A 913 " pdb=" CB VAL A 913 " ideal model delta sigma weight residual 1.541 1.519 0.022 1.28e-02 6.10e+03 3.02e+00 bond pdb=" CA VAL B 914 " pdb=" CB VAL B 914 " ideal model delta sigma weight residual 1.537 1.519 0.018 1.17e-02 7.31e+03 2.43e+00 ... (remaining 11819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15245 2.07 - 4.15: 731 4.15 - 6.22: 110 6.22 - 8.29: 42 8.29 - 10.37: 6 Bond angle restraints: 16134 Sorted by residual: angle pdb=" N PRO A 407 " pdb=" CA PRO A 407 " pdb=" CB PRO A 407 " ideal model delta sigma weight residual 103.15 110.73 -7.58 9.70e-01 1.06e+00 6.11e+01 angle pdb=" N PRO B 407 " pdb=" CA PRO B 407 " pdb=" CB PRO B 407 " ideal model delta sigma weight residual 103.15 110.70 -7.55 9.70e-01 1.06e+00 6.05e+01 angle pdb=" N PRO A 370 " pdb=" CA PRO A 370 " pdb=" CB PRO A 370 " ideal model delta sigma weight residual 103.25 111.19 -7.94 1.05e+00 9.07e-01 5.72e+01 angle pdb=" N PRO B 370 " pdb=" CA PRO B 370 " pdb=" CB PRO B 370 " ideal model delta sigma weight residual 103.25 111.17 -7.92 1.05e+00 9.07e-01 5.69e+01 angle pdb=" N PRO A 308 " pdb=" CA PRO A 308 " pdb=" CB PRO A 308 " ideal model delta sigma weight residual 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.63e+01 ... (remaining 16129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 6494 15.46 - 30.93: 293 30.93 - 46.39: 65 46.39 - 61.85: 6 61.85 - 77.31: 8 Dihedral angle restraints: 6866 sinusoidal: 2052 harmonic: 4814 Sorted by residual: dihedral pdb=" CA VAL B 182 " pdb=" C VAL B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ILE A 138 " pdb=" C ILE A 138 " pdb=" N LEU A 139 " pdb=" CA LEU A 139 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ILE B 138 " pdb=" C ILE B 138 " pdb=" N LEU B 139 " pdb=" CA LEU B 139 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 6863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1617 0.075 - 0.150: 325 0.150 - 0.224: 40 0.224 - 0.299: 4 0.299 - 0.374: 2 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CB ILE A1134 " pdb=" CA ILE A1134 " pdb=" CG1 ILE A1134 " pdb=" CG2 ILE A1134 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE B1134 " pdb=" CA ILE B1134 " pdb=" CG1 ILE B1134 " pdb=" CG2 ILE B1134 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA PRO B 398 " pdb=" N PRO B 398 " pdb=" C PRO B 398 " pdb=" CB PRO B 398 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 1985 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 853 " 0.020 2.00e-02 2.50e+03 1.94e-02 9.40e+00 pdb=" CG TRP B 853 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 853 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 853 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 853 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 853 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 853 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 853 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 853 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 853 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 853 " -0.020 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP A 853 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 853 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 853 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 853 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 853 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 853 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 853 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 853 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 853 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 431 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO B 432 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 432 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 432 " -0.039 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3392 2.81 - 3.33: 10475 3.33 - 3.86: 17674 3.86 - 4.38: 19224 4.38 - 4.90: 33681 Nonbonded interactions: 84446 Sorted by model distance: nonbonded pdb=" OE2 GLU A 102 " pdb=" NH2 ARG A 538 " model vdw 2.291 3.120 nonbonded pdb=" OE2 GLU B 102 " pdb=" NH2 ARG B 538 " model vdw 2.291 3.120 nonbonded pdb=" O THR B 211 " pdb=" OG SER B 525 " model vdw 2.304 3.040 nonbonded pdb=" O THR A 211 " pdb=" OG SER A 525 " model vdw 2.304 3.040 nonbonded pdb=" ND2 ASN A 833 " pdb=" O ASP A1121 " model vdw 2.360 3.120 ... (remaining 84441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.006 0.059 11824 Z= 0.280 Angle : 1.045 10.366 16134 Z= 0.607 Chirality : 0.061 0.374 1988 Planarity : 0.007 0.069 2044 Dihedral : 10.350 77.313 3766 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.38 % Favored : 88.01 % Rotamer: Outliers : 0.40 % Allowed : 5.42 % Favored : 94.18 % 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: -5.55 (0.15), residues: 1652 helix: -3.32 (0.12), residues: 836 sheet: -2.22 (0.43), residues: 142 loop : -4.44 (0.18), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 448 TYR 0.020 0.003 TYR B 678 PHE 0.027 0.003 PHE B 476 TRP 0.052 0.003 TRP A 853 HIS 0.006 0.002 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00600 (11824) covalent geometry : angle 1.04505 (16134) hydrogen bonds : bond 0.17950 ( 514) hydrogen bonds : angle 7.38100 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.8370 (tpt) cc_final: 0.8168 (tpp) REVERT: A 430 TYR cc_start: 0.8921 (t80) cc_final: 0.8709 (t80) REVERT: A 511 VAL cc_start: 0.9263 (m) cc_final: 0.8966 (t) REVERT: A 579 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6604 (mt-10) REVERT: A 850 ASP cc_start: 0.8092 (m-30) cc_final: 0.7839 (m-30) REVERT: B 511 VAL cc_start: 0.9290 (m) cc_final: 0.9033 (t) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.0929 time to fit residues: 32.6886 Evaluate side-chains 136 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 697 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 791 HIS A 840 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 GLN B 618 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094988 restraints weight = 25021.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096999 restraints weight = 15109.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098419 restraints weight = 10738.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099297 restraints weight = 8448.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100021 restraints weight = 7192.203| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11824 Z= 0.140 Angle : 0.625 7.985 16134 Z= 0.331 Chirality : 0.044 0.210 1988 Planarity : 0.005 0.058 2044 Dihedral : 5.738 25.582 1772 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.69 % Favored : 90.07 % Rotamer: Outliers : 3.31 % Allowed : 11.04 % Favored : 85.64 % 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: -4.16 (0.18), residues: 1652 helix: -1.92 (0.16), residues: 834 sheet: -2.30 (0.42), residues: 166 loop : -3.98 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 754 TYR 0.015 0.001 TYR B 422 PHE 0.012 0.001 PHE B 544 TRP 0.015 0.001 TRP A 853 HIS 0.003 0.001 HIS A 742 Details of bonding type rmsd covalent geometry : bond 0.00305 (11824) covalent geometry : angle 0.62457 (16134) hydrogen bonds : bond 0.03886 ( 514) hydrogen bonds : angle 4.80970 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.451 Fit side-chains REVERT: A 511 VAL cc_start: 0.9325 (m) cc_final: 0.9062 (t) REVERT: A 678 TYR cc_start: 0.7819 (m-80) cc_final: 0.7514 (t80) REVERT: B 511 VAL cc_start: 0.9225 (m) cc_final: 0.8983 (t) REVERT: B 512 ILE cc_start: 0.9239 (pp) cc_final: 0.8689 (mm) REVERT: B 579 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6964 (mt-10) REVERT: B 678 TYR cc_start: 0.7705 (m-80) cc_final: 0.7273 (t80) REVERT: B 863 LEU cc_start: 0.8890 (tp) cc_final: 0.8670 (tp) outliers start: 33 outliers final: 17 residues processed: 186 average time/residue: 0.0851 time to fit residues: 24.0730 Evaluate side-chains 150 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.108342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.090876 restraints weight = 25361.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092857 restraints weight = 15114.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094162 restraints weight = 10687.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.095138 restraints weight = 8397.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095848 restraints weight = 7070.317| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11824 Z= 0.217 Angle : 0.666 6.805 16134 Z= 0.349 Chirality : 0.046 0.216 1988 Planarity : 0.004 0.050 2044 Dihedral : 5.624 26.333 1772 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.08 % Favored : 88.68 % Rotamer: Outliers : 3.71 % Allowed : 13.25 % Favored : 83.03 % 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: -3.78 (0.19), residues: 1652 helix: -1.44 (0.17), residues: 854 sheet: -2.32 (0.40), residues: 170 loop : -4.07 (0.21), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.014 0.002 TYR A 422 PHE 0.012 0.001 PHE B 623 TRP 0.028 0.002 TRP A 853 HIS 0.005 0.002 HIS B 870 Details of bonding type rmsd covalent geometry : bond 0.00507 (11824) covalent geometry : angle 0.66630 (16134) hydrogen bonds : bond 0.03909 ( 514) hydrogen bonds : angle 4.56704 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.401 Fit side-chains REVERT: A 446 ASP cc_start: 0.8392 (m-30) cc_final: 0.8162 (m-30) REVERT: A 511 VAL cc_start: 0.9344 (m) cc_final: 0.9083 (t) REVERT: B 511 VAL cc_start: 0.9235 (m) cc_final: 0.8967 (t) REVERT: B 512 ILE cc_start: 0.9273 (pp) cc_final: 0.8611 (mm) REVERT: B 579 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7051 (mt-10) outliers start: 37 outliers final: 25 residues processed: 168 average time/residue: 0.0788 time to fit residues: 21.0189 Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 140 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 0.0970 chunk 125 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A1095 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 HIS B1095 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094631 restraints weight = 24987.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096702 restraints weight = 14728.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098199 restraints weight = 10301.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098991 restraints weight = 7964.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099815 restraints weight = 6794.975| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11824 Z= 0.104 Angle : 0.554 7.417 16134 Z= 0.292 Chirality : 0.042 0.205 1988 Planarity : 0.004 0.046 2044 Dihedral : 4.885 24.056 1768 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.23 % Favored : 91.53 % Rotamer: Outliers : 3.31 % Allowed : 14.76 % Favored : 81.93 % 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: -3.29 (0.20), residues: 1652 helix: -1.01 (0.18), residues: 856 sheet: -2.06 (0.41), residues: 166 loop : -3.91 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.010 0.001 TYR A 422 PHE 0.021 0.001 PHE A 623 TRP 0.007 0.001 TRP A 559 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00224 (11824) covalent geometry : angle 0.55368 (16134) hydrogen bonds : bond 0.02967 ( 514) hydrogen bonds : angle 4.14101 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.401 Fit side-chains REVERT: A 511 VAL cc_start: 0.9329 (m) cc_final: 0.9113 (t) REVERT: A 538 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7885 (mmm-85) REVERT: B 567 ILE cc_start: 0.9213 (mt) cc_final: 0.8996 (mm) REVERT: B 579 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6877 (mt-10) outliers start: 33 outliers final: 21 residues processed: 187 average time/residue: 0.0911 time to fit residues: 25.8524 Evaluate side-chains 159 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 11 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.094617 restraints weight = 24942.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096765 restraints weight = 14639.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098273 restraints weight = 10199.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099162 restraints weight = 7950.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099932 restraints weight = 6763.661| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11824 Z= 0.133 Angle : 0.567 7.045 16134 Z= 0.295 Chirality : 0.043 0.211 1988 Planarity : 0.004 0.041 2044 Dihedral : 4.716 22.883 1768 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.38 % Favored : 90.38 % Rotamer: Outliers : 3.61 % Allowed : 15.06 % 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: -3.06 (0.20), residues: 1652 helix: -0.81 (0.18), residues: 856 sheet: -1.97 (0.41), residues: 166 loop : -3.79 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.009 0.001 TYR A 422 PHE 0.013 0.001 PHE A 623 TRP 0.012 0.001 TRP B 853 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00306 (11824) covalent geometry : angle 0.56662 (16134) hydrogen bonds : bond 0.03005 ( 514) hydrogen bonds : angle 4.08163 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.351 Fit side-chains REVERT: A 511 VAL cc_start: 0.9338 (m) cc_final: 0.9134 (t) REVERT: B 512 ILE cc_start: 0.9232 (pp) cc_final: 0.8595 (mm) REVERT: B 567 ILE cc_start: 0.9287 (mt) cc_final: 0.9054 (mm) REVERT: B 579 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6884 (mt-10) outliers start: 36 outliers final: 22 residues processed: 174 average time/residue: 0.0734 time to fit residues: 20.4171 Evaluate side-chains 161 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 143 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.114121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.096020 restraints weight = 24575.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098173 restraints weight = 14511.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.099684 restraints weight = 10116.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100660 restraints weight = 7842.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101441 restraints weight = 6617.600| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11824 Z= 0.109 Angle : 0.540 5.871 16134 Z= 0.283 Chirality : 0.043 0.222 1988 Planarity : 0.003 0.041 2044 Dihedral : 4.494 21.904 1768 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.46 % Rotamer: Outliers : 2.71 % Allowed : 16.67 % Favored : 80.62 % 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: -2.74 (0.21), residues: 1652 helix: -0.57 (0.18), residues: 862 sheet: -1.82 (0.42), residues: 166 loop : -3.65 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.009 0.001 TYR A 422 PHE 0.012 0.001 PHE B 544 TRP 0.007 0.001 TRP A 798 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00244 (11824) covalent geometry : angle 0.54023 (16134) hydrogen bonds : bond 0.02849 ( 514) hydrogen bonds : angle 3.95539 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.376 Fit side-chains REVERT: B 563 LEU cc_start: 0.9341 (tt) cc_final: 0.9104 (tp) REVERT: B 567 ILE cc_start: 0.9273 (mt) cc_final: 0.9041 (mm) REVERT: B 579 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6855 (mt-10) outliers start: 27 outliers final: 21 residues processed: 173 average time/residue: 0.0750 time to fit residues: 20.4379 Evaluate side-chains 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 169 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 29 optimal weight: 0.0060 chunk 56 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096639 restraints weight = 24542.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098852 restraints weight = 14602.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100342 restraints weight = 10076.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101339 restraints weight = 7854.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101856 restraints weight = 6615.688| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11824 Z= 0.106 Angle : 0.532 7.088 16134 Z= 0.277 Chirality : 0.042 0.218 1988 Planarity : 0.003 0.037 2044 Dihedral : 4.281 21.748 1768 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.84 % Favored : 90.92 % Rotamer: Outliers : 2.91 % Allowed : 17.57 % Favored : 79.52 % 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: -2.51 (0.21), residues: 1652 helix: -0.39 (0.18), residues: 852 sheet: -1.74 (0.42), residues: 166 loop : -3.48 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1127 TYR 0.008 0.001 TYR B 422 PHE 0.010 0.001 PHE B 544 TRP 0.007 0.001 TRP A 798 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00235 (11824) covalent geometry : angle 0.53188 (16134) hydrogen bonds : bond 0.02769 ( 514) hydrogen bonds : angle 3.86938 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.397 Fit side-chains REVERT: B 563 LEU cc_start: 0.9337 (tt) cc_final: 0.9113 (tp) REVERT: B 567 ILE cc_start: 0.9304 (mt) cc_final: 0.9053 (mm) REVERT: B 579 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6882 (mt-10) outliers start: 29 outliers final: 19 residues processed: 178 average time/residue: 0.0720 time to fit residues: 20.1714 Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 163 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096649 restraints weight = 24637.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097869 restraints weight = 16088.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.098952 restraints weight = 11679.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.099310 restraints weight = 9879.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099431 restraints weight = 8931.273| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11824 Z= 0.135 Angle : 0.562 6.870 16134 Z= 0.293 Chirality : 0.044 0.223 1988 Planarity : 0.003 0.037 2044 Dihedral : 4.402 22.119 1768 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.08 % Favored : 90.68 % Rotamer: Outliers : 3.71 % Allowed : 17.97 % Favored : 78.31 % 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: -2.43 (0.21), residues: 1652 helix: -0.30 (0.18), residues: 850 sheet: -1.72 (0.42), residues: 166 loop : -3.47 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 538 TYR 0.008 0.001 TYR A 422 PHE 0.010 0.001 PHE A 623 TRP 0.013 0.001 TRP B 853 HIS 0.004 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00313 (11824) covalent geometry : angle 0.56189 (16134) hydrogen bonds : bond 0.03125 ( 514) hydrogen bonds : angle 3.97358 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.414 Fit side-chains REVERT: B 579 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6794 (mt-10) outliers start: 37 outliers final: 22 residues processed: 173 average time/residue: 0.0743 time to fit residues: 20.7937 Evaluate side-chains 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 45 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.0270 chunk 113 optimal weight: 9.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097735 restraints weight = 24282.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098979 restraints weight = 15761.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099763 restraints weight = 11369.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100360 restraints weight = 9656.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100419 restraints weight = 8843.212| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11824 Z= 0.118 Angle : 0.556 6.919 16134 Z= 0.288 Chirality : 0.043 0.210 1988 Planarity : 0.003 0.037 2044 Dihedral : 4.274 21.428 1768 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.66 % Favored : 91.10 % Rotamer: Outliers : 2.61 % Allowed : 19.28 % Favored : 78.11 % 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: -2.37 (0.21), residues: 1652 helix: -0.22 (0.18), residues: 862 sheet: -1.62 (0.42), residues: 166 loop : -3.55 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.008 0.001 TYR B 422 PHE 0.010 0.001 PHE B 544 TRP 0.008 0.001 TRP B 853 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00268 (11824) covalent geometry : angle 0.55612 (16134) hydrogen bonds : bond 0.02958 ( 514) hydrogen bonds : angle 3.88128 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.381 Fit side-chains REVERT: A 586 MET cc_start: 0.8753 (tpp) cc_final: 0.7945 (tpt) REVERT: B 217 MET cc_start: 0.9218 (ttp) cc_final: 0.8742 (ttt) REVERT: B 579 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6801 (mt-10) outliers start: 26 outliers final: 22 residues processed: 173 average time/residue: 0.0721 time to fit residues: 20.0914 Evaluate side-chains 166 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 8 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 105 optimal weight: 0.0770 chunk 80 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 156 optimal weight: 0.1980 chunk 23 optimal weight: 0.0270 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098303 restraints weight = 24485.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100400 restraints weight = 14761.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101684 restraints weight = 10354.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102772 restraints weight = 8200.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103253 restraints weight = 6898.094| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11824 Z= 0.103 Angle : 0.545 6.791 16134 Z= 0.280 Chirality : 0.042 0.224 1988 Planarity : 0.003 0.050 2044 Dihedral : 4.161 21.603 1768 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.46 % Rotamer: Outliers : 2.21 % Allowed : 19.68 % Favored : 78.11 % 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: -2.13 (0.21), residues: 1652 helix: -0.05 (0.18), residues: 848 sheet: -1.53 (0.43), residues: 166 loop : -3.34 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 99 TYR 0.008 0.001 TYR B 127 PHE 0.011 0.001 PHE A 623 TRP 0.007 0.001 TRP A 559 HIS 0.003 0.001 HIS A 870 Details of bonding type rmsd covalent geometry : bond 0.00227 (11824) covalent geometry : angle 0.54476 (16134) hydrogen bonds : bond 0.02753 ( 514) hydrogen bonds : angle 3.77723 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.394 Fit side-chains REVERT: A 198 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7423 (mt-10) REVERT: A 586 MET cc_start: 0.8650 (tpp) cc_final: 0.8327 (tpt) REVERT: B 198 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7317 (mt-10) REVERT: B 579 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6849 (mt-10) outliers start: 22 outliers final: 18 residues processed: 180 average time/residue: 0.0806 time to fit residues: 22.8335 Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 830 VAL Chi-restraints excluded: chain B residue 879 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 81 optimal weight: 0.0570 chunk 151 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 124 optimal weight: 0.0050 chunk 120 optimal weight: 0.6980 chunk 22 optimal weight: 20.0000 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099324 restraints weight = 24568.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100598 restraints weight = 15683.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101661 restraints weight = 12404.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102077 restraints weight = 9467.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102427 restraints weight = 8901.696| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11824 Z= 0.108 Angle : 0.551 6.830 16134 Z= 0.283 Chirality : 0.043 0.300 1988 Planarity : 0.003 0.039 2044 Dihedral : 4.078 21.807 1768 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.05 % Favored : 91.71 % Rotamer: Outliers : 2.31 % Allowed : 19.98 % Favored : 77.71 % 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: -2.04 (0.21), residues: 1652 helix: 0.02 (0.18), residues: 848 sheet: -1.51 (0.42), residues: 166 loop : -3.28 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 99 TYR 0.008 0.001 TYR B 422 PHE 0.011 0.001 PHE B 544 TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS B 742 Details of bonding type rmsd covalent geometry : bond 0.00241 (11824) covalent geometry : angle 0.55078 (16134) hydrogen bonds : bond 0.02786 ( 514) hydrogen bonds : angle 3.79354 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1641.72 seconds wall clock time: 29 minutes 3.96 seconds (1743.96 seconds total)