Starting phenix.real_space_refine on Tue Jul 29 19:18:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d14_30543/07_2025/7d14_30543_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d14_30543/07_2025/7d14_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_30543/07_2025/7d14_30543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d14_30543/07_2025/7d14_30543.map" model { file = "/net/cci-nas-00/data/ceres_data/7d14_30543/07_2025/7d14_30543_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d14_30543/07_2025/7d14_30543_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 11, 'HIS:plan': 9, 'TYR:plan': 10, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 24, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 493 Restraints were copied for chains: B Time building chain proxies: 12.58, per 1000 atoms: 1.08 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: 3.02 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.27 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: 3.59 Time building geometry restraints manager: 3.45 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: 0.07 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.190 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.003 TRP A 853 HIS 0.006 0.002 HIS A 870 PHE 0.027 0.003 PHE B 476 TYR 0.020 0.003 TYR B 678 ARG 0.004 0.001 ARG A 448 Details of bonding type rmsd hydrogen bonds : bond 0.17950 ( 514) hydrogen bonds : angle 7.38100 ( 1524) covalent geometry : bond 0.00600 (11824) covalent geometry : angle 1.04505 (16134) *********************** 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 : 1.366 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: 0.8964 (t) REVERT: A 579 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6598 (mt-10) REVERT: A 850 ASP cc_start: 0.8092 (m-30) cc_final: 0.7837 (m-30) REVERT: B 511 VAL cc_start: 0.9290 (m) cc_final: 0.9031 (t) REVERT: B 645 MET cc_start: 0.8349 (ttp) cc_final: 0.8145 (ttm) outliers start: 4 outliers final: 2 residues processed: 235 average time/residue: 0.2153 time to fit residues: 74.5446 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 : 1.363 ------------------------------------------------------------------------------- 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 143 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 HIS A 840 ASN B 618 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096059 restraints weight = 25017.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098042 restraints weight = 15440.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099426 restraints weight = 11046.265| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11824 Z= 0.126 Angle : 0.615 8.270 16134 Z= 0.325 Chirality : 0.044 0.216 1988 Planarity : 0.004 0.058 2044 Dihedral : 5.677 25.391 1772 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.69 % Favored : 90.07 % Rotamer: Outliers : 3.41 % Allowed : 10.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.18), residues: 1652 helix: -1.90 (0.16), residues: 834 sheet: -2.29 (0.42), residues: 166 loop : -3.97 (0.21), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 853 HIS 0.003 0.001 HIS A 742 PHE 0.012 0.001 PHE B 544 TYR 0.014 0.001 TYR B 422 ARG 0.005 0.000 ARG A 754 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 514) hydrogen bonds : angle 4.77179 ( 1524) covalent geometry : bond 0.00273 (11824) covalent geometry : angle 0.61482 (16134) *********************** 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 204 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.763 Fit side-chains REVERT: A 511 VAL cc_start: 0.9307 (m) cc_final: 0.9036 (t) REVERT: A 678 TYR cc_start: 0.7790 (m-80) cc_final: 0.7516 (t80) REVERT: B 190 MET cc_start: 0.7605 (ttm) cc_final: 0.7356 (mtp) REVERT: B 511 VAL cc_start: 0.9207 (m) cc_final: 0.8967 (t) REVERT: B 512 ILE cc_start: 0.9226 (pp) cc_final: 0.8685 (mm) REVERT: B 579 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6911 (mt-10) REVERT: B 678 TYR cc_start: 0.7700 (m-80) cc_final: 0.7287 (t80) REVERT: B 863 LEU cc_start: 0.8904 (tp) cc_final: 0.8691 (tp) outliers start: 34 outliers final: 17 residues processed: 197 average time/residue: 0.2242 time to fit residues: 65.4481 Evaluate side-chains 157 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 131 LEU 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 879 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 151 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 791 HIS ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.093550 restraints weight = 25070.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095528 restraints weight = 14841.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097031 restraints weight = 10436.242| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11824 Z= 0.151 Angle : 0.590 6.811 16134 Z= 0.312 Chirality : 0.044 0.216 1988 Planarity : 0.004 0.051 2044 Dihedral : 5.254 24.822 1772 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.62 % Favored : 90.13 % Rotamer: Outliers : 2.71 % Allowed : 13.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.20), residues: 1652 helix: -1.28 (0.17), residues: 840 sheet: -2.17 (0.41), residues: 166 loop : -3.88 (0.21), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 853 HIS 0.004 0.001 HIS A 742 PHE 0.012 0.001 PHE B 623 TYR 0.011 0.001 TYR A 422 ARG 0.005 0.001 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 514) hydrogen bonds : angle 4.35952 ( 1524) covalent geometry : bond 0.00345 (11824) covalent geometry : angle 0.59018 (16134) *********************** 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 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.388 Fit side-chains REVERT: A 446 ASP cc_start: 0.8300 (m-30) cc_final: 0.8016 (m-30) REVERT: A 511 VAL cc_start: 0.9349 (m) cc_final: 0.9128 (t) REVERT: B 511 VAL cc_start: 0.9223 (m) cc_final: 0.8986 (t) REVERT: B 512 ILE cc_start: 0.9247 (pp) cc_final: 0.8689 (mm) REVERT: B 579 GLU cc_start: 0.7271 (mt-10) cc_final: 0.7000 (mt-10) outliers start: 27 outliers final: 16 residues processed: 173 average time/residue: 0.1902 time to fit residues: 51.5936 Evaluate side-chains 156 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 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 570 ILE 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 280 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 545 LEU 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 106 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.093901 restraints weight = 24867.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095955 restraints weight = 14810.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097277 restraints weight = 10390.967| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11824 Z= 0.132 Angle : 0.570 6.032 16134 Z= 0.300 Chirality : 0.044 0.209 1988 Planarity : 0.004 0.045 2044 Dihedral : 4.924 24.015 1768 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.08 % Favored : 90.68 % Rotamer: Outliers : 3.31 % Allowed : 14.36 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.20), residues: 1652 helix: -0.94 (0.18), residues: 854 sheet: -2.08 (0.40), residues: 166 loop : -3.78 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 853 HIS 0.004 0.001 HIS B 742 PHE 0.020 0.001 PHE A 623 TYR 0.010 0.001 TYR B 422 ARG 0.005 0.000 ARG A 774 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 514) hydrogen bonds : angle 4.16428 ( 1524) covalent geometry : bond 0.00302 (11824) covalent geometry : angle 0.56950 (16134) *********************** 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 187 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 1.416 Fit side-chains REVERT: A 446 ASP cc_start: 0.8285 (m-30) cc_final: 0.8079 (m-30) REVERT: A 511 VAL cc_start: 0.9358 (m) cc_final: 0.9139 (t) REVERT: B 511 VAL cc_start: 0.9236 (m) cc_final: 0.9027 (t) REVERT: B 512 ILE cc_start: 0.9251 (pp) cc_final: 0.8648 (mm) REVERT: B 567 ILE cc_start: 0.9231 (mt) cc_final: 0.8978 (mm) REVERT: B 579 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6909 (mt-10) outliers start: 33 outliers final: 21 residues processed: 177 average time/residue: 0.1863 time to fit residues: 51.8931 Evaluate side-chains 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 253 MET Chi-restraints excluded: chain A residue 280 LEU 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 512 ILE Chi-restraints excluded: chain A residue 570 ILE 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 143 LEU 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 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 51 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 104 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN B 720 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095783 restraints weight = 24743.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097323 restraints weight = 15552.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098105 restraints weight = 11389.229| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11824 Z= 0.132 Angle : 0.559 6.399 16134 Z= 0.293 Chirality : 0.043 0.212 1988 Planarity : 0.004 0.047 2044 Dihedral : 4.698 23.513 1768 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.44 % Favored : 90.31 % Rotamer: Outliers : 3.31 % Allowed : 14.96 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1652 helix: -0.72 (0.18), residues: 850 sheet: -1.97 (0.40), residues: 166 loop : -3.62 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 853 HIS 0.004 0.001 HIS B 742 PHE 0.012 0.001 PHE A 623 TYR 0.010 0.001 TYR A 422 ARG 0.005 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 514) hydrogen bonds : angle 4.07986 ( 1524) covalent geometry : bond 0.00305 (11824) covalent geometry : angle 0.55903 (16134) *********************** 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 190 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.436 Fit side-chains REVERT: A 446 ASP cc_start: 0.8306 (m-30) cc_final: 0.8097 (m-30) REVERT: A 511 VAL cc_start: 0.9347 (m) cc_final: 0.9130 (t) REVERT: A 512 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 512 ILE cc_start: 0.9256 (pp) cc_final: 0.8598 (mm) REVERT: B 567 ILE cc_start: 0.9269 (mt) cc_final: 0.9051 (mm) REVERT: B 579 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6818 (mt-10) outliers start: 33 outliers final: 23 residues processed: 179 average time/residue: 0.1774 time to fit residues: 50.6878 Evaluate side-chains 167 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 253 MET Chi-restraints excluded: chain A residue 280 LEU 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 512 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 756 MET 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 219 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 288 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 61 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 37 optimal weight: 0.0060 chunk 142 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.096195 restraints weight = 24913.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.098396 restraints weight = 14585.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099889 restraints weight = 10069.161| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3003 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= 0.111 Angle : 0.543 6.571 16134 Z= 0.284 Chirality : 0.043 0.219 1988 Planarity : 0.003 0.040 2044 Dihedral : 4.493 21.749 1768 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.60 % Favored : 91.16 % Rotamer: Outliers : 2.91 % Allowed : 17.37 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1652 helix: -0.55 (0.18), residues: 850 sheet: -1.85 (0.41), residues: 166 loop : -3.52 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 853 HIS 0.004 0.001 HIS B 742 PHE 0.012 0.001 PHE A 544 TYR 0.009 0.001 TYR A 422 ARG 0.005 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 514) hydrogen bonds : angle 3.97189 ( 1524) covalent geometry : bond 0.00250 (11824) covalent geometry : angle 0.54315 (16134) *********************** 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 192 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.390 Fit side-chains REVERT: A 512 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8785 (mm) REVERT: B 264 MET cc_start: 0.8752 (ptm) cc_final: 0.8504 (ptp) REVERT: B 512 ILE cc_start: 0.9292 (pp) cc_final: 0.8680 (mm) REVERT: B 563 LEU cc_start: 0.9357 (tt) cc_final: 0.9115 (tp) REVERT: B 567 ILE cc_start: 0.9269 (mt) cc_final: 0.9039 (mm) REVERT: B 579 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6851 (mt-10) outliers start: 29 outliers final: 19 residues processed: 185 average time/residue: 0.1868 time to fit residues: 54.0926 Evaluate side-chains 166 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 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 512 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 577 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 280 LEU Chi-restraints excluded: chain B residue 288 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 24 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 167 optimal weight: 0.0370 chunk 108 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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** ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097814 restraints weight = 24796.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098981 restraints weight = 15782.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100026 restraints weight = 12399.512| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11824 Z= 0.111 Angle : 0.534 6.413 16134 Z= 0.278 Chirality : 0.042 0.222 1988 Planarity : 0.003 0.036 2044 Dihedral : 4.324 21.603 1768 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.54 % Favored : 91.22 % Rotamer: Outliers : 2.91 % Allowed : 18.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.21), residues: 1652 helix: -0.41 (0.18), residues: 852 sheet: -1.74 (0.42), residues: 166 loop : -3.49 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 853 HIS 0.004 0.001 HIS B 742 PHE 0.012 0.001 PHE A 544 TYR 0.008 0.001 TYR B 422 ARG 0.004 0.000 ARG A1127 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 514) hydrogen bonds : angle 3.91303 ( 1524) covalent geometry : bond 0.00250 (11824) covalent geometry : angle 0.53355 (16134) *********************** 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 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.368 Fit side-chains REVERT: A 590 MET cc_start: 0.8712 (tpp) cc_final: 0.8460 (mtt) REVERT: B 563 LEU cc_start: 0.9370 (tt) cc_final: 0.9127 (tp) REVERT: B 567 ILE cc_start: 0.9298 (mt) cc_final: 0.9048 (mm) REVERT: B 579 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6740 (mt-10) outliers start: 29 outliers final: 24 residues processed: 170 average time/residue: 0.1773 time to fit residues: 47.8161 Evaluate side-chains 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU 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 253 MET Chi-restraints excluded: chain A residue 280 LEU 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 756 MET 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 288 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 33 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097350 restraints weight = 24657.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098685 restraints weight = 15946.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099801 restraints weight = 11487.967| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3303 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= 0.120 Angle : 0.547 6.852 16134 Z= 0.286 Chirality : 0.043 0.307 1988 Planarity : 0.003 0.037 2044 Dihedral : 4.315 21.493 1768 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.90 % Favored : 90.86 % Rotamer: Outliers : 3.31 % Allowed : 19.28 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1652 helix: -0.34 (0.18), residues: 858 sheet: -1.66 (0.42), residues: 166 loop : -3.52 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 853 HIS 0.004 0.001 HIS B 742 PHE 0.012 0.001 PHE A 544 TYR 0.008 0.001 TYR B 422 ARG 0.003 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 514) hydrogen bonds : angle 3.90076 ( 1524) covalent geometry : bond 0.00273 (11824) covalent geometry : angle 0.54718 (16134) *********************** 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: 33 poor density : 154 time to evaluate : 1.265 Fit side-chains REVERT: A 590 MET cc_start: 0.8584 (tpp) cc_final: 0.8260 (mtt) REVERT: B 579 GLU cc_start: 0.7054 (mt-10) cc_final: 0.6750 (mt-10) outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 0.1775 time to fit residues: 49.5842 Evaluate side-chains 170 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 219 ILE 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 474 VAL 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 756 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 127 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 110 optimal weight: 10.0000 chunk 139 optimal weight: 0.3980 chunk 109 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** 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 = 0.114843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098456 restraints weight = 24608.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.099647 restraints weight = 15481.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100724 restraints weight = 12059.127| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11824 Z= 0.116 Angle : 0.556 7.204 16134 Z= 0.287 Chirality : 0.043 0.278 1988 Planarity : 0.003 0.036 2044 Dihedral : 4.246 20.872 1768 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.84 % Favored : 90.92 % Rotamer: Outliers : 2.71 % Allowed : 19.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.21), residues: 1652 helix: -0.23 (0.18), residues: 858 sheet: -1.58 (0.42), residues: 166 loop : -3.47 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 853 HIS 0.003 0.001 HIS B 742 PHE 0.012 0.001 PHE A 544 TYR 0.008 0.001 TYR B 422 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02962 ( 514) hydrogen bonds : angle 3.86568 ( 1524) covalent geometry : bond 0.00264 (11824) covalent geometry : angle 0.55606 (16134) *********************** 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 178 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.250 Fit side-chains REVERT: B 217 MET cc_start: 0.9180 (ttp) cc_final: 0.8696 (ttt) REVERT: B 579 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6745 (mt-10) outliers start: 27 outliers final: 22 residues processed: 169 average time/residue: 0.1875 time to fit residues: 50.6539 Evaluate side-chains 170 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 474 VAL 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 756 MET 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 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 164 optimal weight: 0.0470 chunk 90 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 47 optimal weight: 0.0060 chunk 29 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.4294 ------------------------------------------------------------------------------- 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 B 602 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099996 restraints weight = 24362.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101246 restraints weight = 15171.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102109 restraints weight = 10902.133| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3551 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 : 0.550 7.341 16134 Z= 0.283 Chirality : 0.043 0.270 1988 Planarity : 0.003 0.037 2044 Dihedral : 4.128 21.419 1768 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.41 % Favored : 91.34 % Rotamer: Outliers : 2.41 % Allowed : 20.08 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.21), residues: 1652 helix: -0.11 (0.18), residues: 856 sheet: -1.54 (0.42), residues: 166 loop : -3.39 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 619 HIS 0.003 0.001 HIS B 742 PHE 0.012 0.001 PHE A 544 TYR 0.008 0.001 TYR B 422 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 514) hydrogen bonds : angle 3.78929 ( 1524) covalent geometry : bond 0.00226 (11824) covalent geometry : angle 0.54972 (16134) ********************** 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 189 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.341 Fit side-chains REVERT: A 249 MET cc_start: 0.8359 (tpp) cc_final: 0.8091 (tpp) REVERT: A 586 MET cc_start: 0.8409 (tpp) cc_final: 0.8064 (tpt) REVERT: B 198 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7308 (mt-10) REVERT: B 579 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6792 (mt-10) REVERT: B 586 MET cc_start: 0.8533 (tpp) cc_final: 0.7841 (tpt) outliers start: 24 outliers final: 22 residues processed: 182 average time/residue: 0.1928 time to fit residues: 54.3787 Evaluate side-chains 174 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 709 VAL Chi-restraints excluded: chain A residue 756 MET 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 55 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 163 optimal weight: 0.0670 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099186 restraints weight = 24415.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100502 restraints weight = 15288.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101727 restraints weight = 10977.111| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11824 Z= 0.112 Angle : 0.561 9.023 16134 Z= 0.287 Chirality : 0.042 0.266 1988 Planarity : 0.003 0.050 2044 Dihedral : 4.080 21.750 1768 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.46 % Rotamer: Outliers : 2.41 % Allowed : 20.58 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.21), residues: 1652 helix: 0.02 (0.18), residues: 848 sheet: -1.48 (0.42), residues: 166 loop : -3.29 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 798 HIS 0.003 0.001 HIS B 742 PHE 0.012 0.001 PHE A 544 TYR 0.008 0.001 TYR B 422 ARG 0.009 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 514) hydrogen bonds : angle 3.78916 ( 1524) covalent geometry : bond 0.00252 (11824) covalent geometry : angle 0.56114 (16134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.50 seconds wall clock time: 59 minutes 8.58 seconds (3548.58 seconds total)