Starting phenix.real_space_refine on Wed Mar 4 18:32:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k1p_9719/03_2026/6k1p_9719.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k1p_9719/03_2026/6k1p_9719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k1p_9719/03_2026/6k1p_9719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k1p_9719/03_2026/6k1p_9719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k1p_9719/03_2026/6k1p_9719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k1p_9719/03_2026/6k1p_9719.map" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9070 2.51 5 N 2911 2.21 5 O 3536 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15841 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3794 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 17, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.25, per 1000 atoms: 0.21 Number of scatterers: 15841 At special positions: 0 Unit cell: (144.45, 129.47, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3536 8.00 N 2911 7.00 C 9070 6.00 Be 1 4.00 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: 1.07 Conformation dependent library (CDL) restraints added in 384.3 milliseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 60.5% alpha, 3.3% beta 144 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.612A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.839A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.964A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.985A pdb=" N ARG B 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 20 " --> pdb=" O ARG B 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 20' Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.393A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.696A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.710A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.545A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.538A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 4.039A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 120 removed outlier: 4.020A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.549A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.578A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.743A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.610A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.742A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.432A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.628A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.670A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.659A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.706A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU G 116 " --> pdb=" O SER G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.974A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 120 removed outlier: 3.815A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 211 removed outlier: 3.580A pdb=" N TRP K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 207 " --> pdb=" O GLY K 203 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER K 209 " --> pdb=" O ASN K 205 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU K 210 " --> pdb=" O TRP K 206 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS K 211 " --> pdb=" O LEU K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 241 removed outlier: 3.655A pdb=" N GLN K 230 " --> pdb=" O GLY K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.705A pdb=" N TRP K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG K 262 " --> pdb=" O ASN K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 288 Processing helix chain 'K' and resid 334 through 340 Processing helix chain 'K' and resid 362 through 369 removed outlier: 3.584A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 383 removed outlier: 3.742A pdb=" N ASP K 382 " --> pdb=" O ALA K 378 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP K 383 " --> pdb=" O GLN K 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 378 through 383' Processing helix chain 'K' and resid 396 through 402 removed outlier: 3.614A pdb=" N LEU K 401 " --> pdb=" O ILE K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 409 removed outlier: 3.769A pdb=" N PHE K 408 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU K 409 " --> pdb=" O GLN K 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 405 through 409' Processing helix chain 'K' and resid 413 through 418 removed outlier: 3.780A pdb=" N VAL K 417 " --> pdb=" O ILE K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 removed outlier: 3.524A pdb=" N LYS K 443 " --> pdb=" O LYS K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 476 removed outlier: 3.826A pdb=" N GLN K 471 " --> pdb=" O ASN K 467 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 483 removed outlier: 4.074A pdb=" N LEU K 481 " --> pdb=" O HIS K 478 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE K 482 " --> pdb=" O PRO K 479 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 483 " --> pdb=" O TYR K 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 478 through 483' Processing helix chain 'K' and resid 496 through 501 removed outlier: 3.820A pdb=" N ALA K 501 " --> pdb=" O LEU K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 518 removed outlier: 3.563A pdb=" N LYS K 509 " --> pdb=" O GLN K 505 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 539 removed outlier: 3.865A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR K 539 " --> pdb=" O GLU K 535 " (cutoff:3.500A) Processing helix chain 'K' and resid 554 through 565 removed outlier: 3.531A pdb=" N ILE K 558 " --> pdb=" O HIS K 554 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN K 559 " --> pdb=" O GLU K 555 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE K 561 " --> pdb=" O ARG K 557 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP K 562 " --> pdb=" O ILE K 558 " (cutoff:3.500A) Processing helix chain 'K' and resid 577 through 582 Processing helix chain 'K' and resid 601 through 610 removed outlier: 4.261A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU K 606 " --> pdb=" O PRO K 602 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP K 610 " --> pdb=" O LEU K 606 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 656 removed outlier: 3.610A pdb=" N ALA K 640 " --> pdb=" O ILE K 636 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN K 642 " --> pdb=" O GLU K 638 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS K 643 " --> pdb=" O ARG K 639 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 644 " --> pdb=" O ALA K 640 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN K 652 " --> pdb=" O GLN K 648 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN K 653 " --> pdb=" O LEU K 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.377A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.753A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.986A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.151A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 300 through 302 removed outlier: 6.496A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 425 through 431 removed outlier: 6.242A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ARG K 625 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 593 " --> pdb=" O PHE K 624 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU K 626 " --> pdb=" O VAL K 593 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU K 595 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR K 628 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU K 522 " --> pdb=" O VAL K 594 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 455 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2929 1.33 - 1.45: 5243 1.45 - 1.57: 7919 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 16722 Sorted by residual: bond pdb=" F2 BEF K1201 " pdb="BE BEF K1201 " ideal model delta sigma weight residual 1.476 1.708 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" F1 BEF K1201 " pdb="BE BEF K1201 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" F3 BEF K1201 " pdb="BE BEF K1201 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.508 -0.086 3.00e-02 1.11e+03 8.25e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.15e+00 ... (remaining 16717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 23716 4.26 - 8.52: 133 8.52 - 12.77: 6 12.77 - 17.03: 1 17.03 - 21.29: 1 Bond angle restraints: 23857 Sorted by residual: angle pdb=" F1 BEF K1201 " pdb="BE BEF K1201 " pdb=" F3 BEF K1201 " ideal model delta sigma weight residual 120.12 98.83 21.29 3.00e+00 1.11e-01 5.04e+01 angle pdb=" N PHE K 248 " pdb=" CA PHE K 248 " pdb=" C PHE K 248 " ideal model delta sigma weight residual 111.02 118.82 -7.80 1.25e+00 6.40e-01 3.89e+01 angle pdb=" N ILE K 275 " pdb=" CA ILE K 275 " pdb=" C ILE K 275 " ideal model delta sigma weight residual 109.34 98.85 10.49 2.08e+00 2.31e-01 2.54e+01 angle pdb=" N ALA K 273 " pdb=" CA ALA K 273 " pdb=" C ALA K 273 " ideal model delta sigma weight residual 108.38 115.06 -6.68 1.35e+00 5.49e-01 2.45e+01 angle pdb=" F2 BEF K1201 " pdb="BE BEF K1201 " pdb=" F3 BEF K1201 " ideal model delta sigma weight residual 119.96 105.14 14.82 3.00e+00 1.11e-01 2.44e+01 ... (remaining 23852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 7787 32.67 - 65.33: 1519 65.33 - 98.00: 16 98.00 - 130.67: 2 130.67 - 163.34: 4 Dihedral angle restraints: 9328 sinusoidal: 5735 harmonic: 3593 Sorted by residual: dihedral pdb=" C5' ADP K1203 " pdb=" O5' ADP K1203 " pdb=" PA ADP K1203 " pdb=" O2A ADP K1203 " ideal model delta sinusoidal sigma weight residual -60.00 80.71 -140.70 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O2A ADP K1203 " pdb=" O3A ADP K1203 " pdb=" PA ADP K1203 " pdb=" PB ADP K1203 " ideal model delta sinusoidal sigma weight residual -60.00 71.04 -131.04 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP K1203 " pdb=" O3A ADP K1203 " pdb=" PB ADP K1203 " pdb=" PA ADP K1203 " ideal model delta sinusoidal sigma weight residual -60.00 63.66 -123.66 1 2.00e+01 2.50e-03 3.73e+01 ... (remaining 9325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2086 0.065 - 0.129: 548 0.129 - 0.194: 64 0.194 - 0.258: 10 0.258 - 0.323: 4 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA ILE K 275 " pdb=" N ILE K 275 " pdb=" C ILE K 275 " pdb=" CB ILE K 275 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ASN K 542 " pdb=" N ASN K 542 " pdb=" C ASN K 542 " pdb=" CB ASN K 542 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP K 494 " pdb=" N ASP K 494 " pdb=" C ASP K 494 " pdb=" CB ASP K 494 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2709 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " 0.034 2.00e-02 2.50e+03 1.44e-02 5.74e+00 pdb=" N9 DA I 91 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO D 100 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.032 2.00e-02 2.50e+03 1.49e-02 5.56e+00 pdb=" N1 DT I 88 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " -0.017 2.00e-02 2.50e+03 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 35 2.45 - 3.06: 9090 3.06 - 3.68: 24788 3.68 - 4.29: 37458 4.29 - 4.90: 54792 Nonbonded interactions: 126163 Sorted by model distance: nonbonded pdb=" O SER D 33 " pdb=" CD1 TYR D 34 " model vdw 1.838 3.340 nonbonded pdb=" O GLY K 584 " pdb=" F2 BEF K1201 " model vdw 2.196 2.990 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.283 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.287 3.120 nonbonded pdb=" OD1 ASP K 494 " pdb=" N HIS K 496 " model vdw 2.309 3.120 ... (remaining 126158 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.010 0.232 16722 Z= 0.427 Angle : 1.035 21.289 23857 Z= 0.578 Chirality : 0.057 0.323 2712 Planarity : 0.007 0.060 2012 Dihedral : 24.900 163.335 7002 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.51 % Favored : 90.91 % Rotamer: Outliers : 0.10 % Allowed : 1.34 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.18), residues: 1210 helix: -2.64 (0.14), residues: 687 sheet: -2.80 (0.71), residues: 49 loop : -3.29 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 35 TYR 0.039 0.004 TYR H 37 PHE 0.033 0.004 PHE F 100 TRP 0.032 0.003 TRP K 267 HIS 0.010 0.002 HIS K 327 Details of bonding type rmsd covalent geometry : bond 0.00977 (16722) covalent geometry : angle 1.03467 (23857) hydrogen bonds : bond 0.16283 ( 824) hydrogen bonds : angle 5.78747 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8660 (m-10) cc_final: 0.8228 (m-80) REVERT: C 74 LYS cc_start: 0.8910 (mttt) cc_final: 0.8506 (pttm) REVERT: D 80 TYR cc_start: 0.8056 (m-10) cc_final: 0.7772 (m-10) REVERT: F 88 TYR cc_start: 0.8739 (m-10) cc_final: 0.7965 (m-80) REVERT: G 90 ASP cc_start: 0.8537 (t70) cc_final: 0.7580 (t0) REVERT: G 95 LYS cc_start: 0.8617 (tptm) cc_final: 0.8348 (mtpp) REVERT: H 80 TYR cc_start: 0.7648 (m-10) cc_final: 0.6920 (m-10) REVERT: K 350 LEU cc_start: 0.8984 (tp) cc_final: 0.8703 (tp) REVERT: K 351 ILE cc_start: 0.8521 (mt) cc_final: 0.8302 (pt) REVERT: K 362 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7232 (mt-10) REVERT: K 470 MET cc_start: 0.8401 (tpt) cc_final: 0.8085 (tpp) REVERT: K 511 LEU cc_start: 0.8520 (mt) cc_final: 0.8199 (tt) REVERT: K 527 MET cc_start: 0.7930 (mtm) cc_final: 0.7710 (mtp) REVERT: K 599 ASP cc_start: 0.7596 (t0) cc_final: 0.6921 (t0) REVERT: K 635 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7775 (mtmm) REVERT: K 648 GLN cc_start: 0.7559 (tp-100) cc_final: 0.7004 (tm-30) outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.1558 time to fit residues: 57.7956 Evaluate side-chains 164 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 125 GLN B 93 GLN C 38 ASN D 46 HIS D 81 ASN E 68 GLN G 38 ASN H 81 ASN K 205 ASN ** K 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN K 477 ASN K 526 GLN ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100050 restraints weight = 31086.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.100557 restraints weight = 18885.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101055 restraints weight = 15315.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101417 restraints weight = 13615.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101579 restraints weight = 12952.135| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16722 Z= 0.181 Angle : 0.670 7.885 23857 Z= 0.377 Chirality : 0.039 0.247 2712 Planarity : 0.005 0.070 2012 Dihedral : 28.980 162.060 4560 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.63 % Allowed : 10.81 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.23), residues: 1210 helix: -0.64 (0.18), residues: 718 sheet: -2.42 (0.76), residues: 50 loop : -3.08 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 639 TYR 0.020 0.002 TYR D 37 PHE 0.017 0.002 PHE K 375 TRP 0.019 0.001 TRP K 267 HIS 0.004 0.001 HIS K 327 Details of bonding type rmsd covalent geometry : bond 0.00398 (16722) covalent geometry : angle 0.66962 (23857) hydrogen bonds : bond 0.05937 ( 824) hydrogen bonds : angle 3.57068 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8700 (m-10) cc_final: 0.8436 (m-80) REVERT: E 118 THR cc_start: 0.9472 (m) cc_final: 0.8962 (p) REVERT: G 95 LYS cc_start: 0.8595 (tptm) cc_final: 0.8362 (mtpp) REVERT: H 30 ARG cc_start: 0.7839 (ptp90) cc_final: 0.7436 (ptp-170) REVERT: H 80 TYR cc_start: 0.7308 (m-10) cc_final: 0.7072 (m-10) REVERT: K 335 MET cc_start: 0.8467 (tpp) cc_final: 0.8092 (tpp) REVERT: K 350 LEU cc_start: 0.8866 (tp) cc_final: 0.8364 (tt) REVERT: K 351 ILE cc_start: 0.8548 (mt) cc_final: 0.8264 (mt) REVERT: K 470 MET cc_start: 0.8296 (tpt) cc_final: 0.7912 (tpp) REVERT: K 599 ASP cc_start: 0.7427 (t0) cc_final: 0.6794 (t0) outliers start: 17 outliers final: 10 residues processed: 196 average time/residue: 0.1228 time to fit residues: 35.6402 Evaluate side-chains 173 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 123 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN F 25 ASN K 211 HIS ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.134272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.095384 restraints weight = 31556.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097461 restraints weight = 19383.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098785 restraints weight = 14387.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.099560 restraints weight = 12171.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099998 restraints weight = 11124.689| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16722 Z= 0.171 Angle : 0.615 8.152 23857 Z= 0.348 Chirality : 0.038 0.224 2712 Planarity : 0.005 0.053 2012 Dihedral : 28.752 161.820 4559 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.12 % Favored : 93.80 % Rotamer: Outliers : 2.78 % Allowed : 12.25 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.24), residues: 1210 helix: 0.29 (0.20), residues: 719 sheet: -2.47 (0.71), residues: 55 loop : -2.69 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 655 TYR 0.020 0.002 TYR D 37 PHE 0.020 0.002 PHE K 375 TRP 0.007 0.001 TRP K 267 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (16722) covalent geometry : angle 0.61539 (23857) hydrogen bonds : bond 0.05099 ( 824) hydrogen bonds : angle 3.22384 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 GLU cc_start: 0.6390 (tp30) cc_final: 0.5997 (tp30) REVERT: E 76 GLN cc_start: 0.8246 (pp30) cc_final: 0.7821 (tm-30) REVERT: E 77 ASP cc_start: 0.8330 (m-30) cc_final: 0.7552 (t0) REVERT: G 25 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: G 95 LYS cc_start: 0.8632 (tptm) cc_final: 0.8414 (mtpp) REVERT: H 30 ARG cc_start: 0.7706 (ptp90) cc_final: 0.7375 (ptp-170) REVERT: H 80 TYR cc_start: 0.7289 (m-10) cc_final: 0.7086 (m-10) REVERT: H 102 GLU cc_start: 0.7535 (tp30) cc_final: 0.6334 (tp30) REVERT: K 276 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8329 (tt) REVERT: K 327 HIS cc_start: 0.7697 (m90) cc_final: 0.7460 (p-80) REVERT: K 335 MET cc_start: 0.8541 (tpp) cc_final: 0.8059 (tpp) REVERT: K 350 LEU cc_start: 0.8811 (tp) cc_final: 0.8477 (tt) REVERT: K 352 THR cc_start: 0.8405 (t) cc_final: 0.7866 (m) REVERT: K 599 ASP cc_start: 0.7634 (t0) cc_final: 0.7059 (t0) outliers start: 29 outliers final: 15 residues processed: 188 average time/residue: 0.1112 time to fit residues: 31.2882 Evaluate side-chains 173 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 25 PHE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 HIS ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.145742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111075 restraints weight = 31789.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112722 restraints weight = 21132.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112788 restraints weight = 16189.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113248 restraints weight = 15377.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113231 restraints weight = 13402.994| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16722 Z= 0.129 Angle : 0.566 15.054 23857 Z= 0.319 Chirality : 0.035 0.263 2712 Planarity : 0.004 0.045 2012 Dihedral : 28.412 162.456 4559 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 2.11 % Allowed : 14.07 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1210 helix: 0.92 (0.20), residues: 728 sheet: -2.11 (0.82), residues: 41 loop : -2.39 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 655 TYR 0.015 0.001 TYR K 537 PHE 0.021 0.001 PHE K 375 TRP 0.012 0.001 TRP K 384 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00270 (16722) covalent geometry : angle 0.56612 (23857) hydrogen bonds : bond 0.03819 ( 824) hydrogen bonds : angle 2.72988 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.7838 (tt0) cc_final: 0.7609 (tt0) REVERT: E 76 GLN cc_start: 0.8232 (pp30) cc_final: 0.7921 (tm-30) REVERT: E 77 ASP cc_start: 0.8120 (m-30) cc_final: 0.7385 (t0) REVERT: E 109 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8797 (tp) REVERT: H 30 ARG cc_start: 0.7648 (ptp90) cc_final: 0.7363 (ptp-170) REVERT: H 102 GLU cc_start: 0.7575 (tp30) cc_final: 0.7365 (tp30) REVERT: H 105 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7336 (mtpt) REVERT: K 599 ASP cc_start: 0.7498 (t0) cc_final: 0.7005 (t0) outliers start: 22 outliers final: 4 residues processed: 199 average time/residue: 0.1180 time to fit residues: 34.8441 Evaluate side-chains 155 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain K residue 356 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN D 106 HIS F 25 ASN F 93 GLN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 601 ASN K 620 GLN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096876 restraints weight = 31175.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098903 restraints weight = 19330.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100245 restraints weight = 14445.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.101012 restraints weight = 12219.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101375 restraints weight = 11203.312| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16722 Z= 0.188 Angle : 0.609 8.285 23857 Z= 0.342 Chirality : 0.037 0.225 2712 Planarity : 0.004 0.040 2012 Dihedral : 28.559 161.959 4559 Min Nonbonded Distance : 1.663 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 2.39 % Allowed : 15.98 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1210 helix: 0.96 (0.20), residues: 730 sheet: -2.34 (0.75), residues: 49 loop : -2.30 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 49 TYR 0.015 0.002 TYR C 57 PHE 0.016 0.002 PHE K 375 TRP 0.006 0.001 TRP K 384 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (16722) covalent geometry : angle 0.60904 (23857) hydrogen bonds : bond 0.05165 ( 824) hydrogen bonds : angle 3.04825 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.7934 (tt0) cc_final: 0.7639 (tt0) REVERT: E 76 GLN cc_start: 0.8387 (pp30) cc_final: 0.7974 (tm-30) REVERT: E 77 ASP cc_start: 0.8244 (m-30) cc_final: 0.7384 (t0) REVERT: H 30 ARG cc_start: 0.7710 (ptp90) cc_final: 0.7426 (ptp-170) REVERT: K 350 LEU cc_start: 0.8794 (tp) cc_final: 0.8469 (tt) REVERT: K 599 ASP cc_start: 0.7604 (t0) cc_final: 0.7030 (t0) outliers start: 25 outliers final: 16 residues processed: 164 average time/residue: 0.1100 time to fit residues: 27.6491 Evaluate side-chains 155 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN F 25 ASN H 81 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098968 restraints weight = 31193.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101045 restraints weight = 19148.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102358 restraints weight = 14285.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103222 restraints weight = 12123.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103641 restraints weight = 11090.141| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16722 Z= 0.147 Angle : 0.573 12.290 23857 Z= 0.322 Chirality : 0.035 0.218 2712 Planarity : 0.004 0.038 2012 Dihedral : 28.406 161.789 4559 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.79 % Rotamer: Outliers : 2.78 % Allowed : 16.65 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1210 helix: 1.24 (0.20), residues: 730 sheet: -2.23 (0.76), residues: 49 loop : -2.25 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.026 0.001 TYR H 80 PHE 0.015 0.001 PHE K 375 TRP 0.018 0.001 TRP K 384 HIS 0.003 0.001 HIS K 554 Details of bonding type rmsd covalent geometry : bond 0.00322 (16722) covalent geometry : angle 0.57337 (23857) hydrogen bonds : bond 0.04418 ( 824) hydrogen bonds : angle 2.80105 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8900 (p) cc_final: 0.8554 (t) REVERT: E 76 GLN cc_start: 0.8429 (pp30) cc_final: 0.8005 (tt0) REVERT: E 77 ASP cc_start: 0.8201 (m-30) cc_final: 0.7439 (t0) REVERT: H 30 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7451 (ptp-170) REVERT: H 113 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8286 (mtmm) REVERT: K 350 LEU cc_start: 0.8711 (tp) cc_final: 0.8350 (tt) REVERT: K 599 ASP cc_start: 0.7626 (t0) cc_final: 0.7115 (t0) outliers start: 29 outliers final: 16 residues processed: 167 average time/residue: 0.1081 time to fit residues: 27.6354 Evaluate side-chains 166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 534 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 81 ASN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096730 restraints weight = 30936.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097115 restraints weight = 18807.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.097712 restraints weight = 15145.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097774 restraints weight = 14408.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.098167 restraints weight = 13272.126| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16722 Z= 0.239 Angle : 0.661 7.469 23857 Z= 0.366 Chirality : 0.040 0.277 2712 Planarity : 0.005 0.039 2012 Dihedral : 28.629 160.713 4559 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.44 % Favored : 92.48 % Rotamer: Outliers : 3.44 % Allowed : 16.94 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.25), residues: 1210 helix: 1.03 (0.20), residues: 728 sheet: -2.32 (0.75), residues: 49 loop : -2.41 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 35 TYR 0.051 0.002 TYR H 80 PHE 0.013 0.002 PHE K 375 TRP 0.022 0.002 TRP K 384 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00552 (16722) covalent geometry : angle 0.66060 (23857) hydrogen bonds : bond 0.05908 ( 824) hydrogen bonds : angle 3.26114 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8910 (p) cc_final: 0.8598 (t) REVERT: D 98 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8348 (mm) REVERT: E 76 GLN cc_start: 0.8474 (pp30) cc_final: 0.8012 (tt0) REVERT: E 77 ASP cc_start: 0.8275 (m-30) cc_final: 0.7269 (t0) REVERT: F 25 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8077 (t0) REVERT: H 30 ARG cc_start: 0.7815 (ptp90) cc_final: 0.7455 (ptp-170) REVERT: K 350 LEU cc_start: 0.8806 (tp) cc_final: 0.8423 (tt) REVERT: K 527 MET cc_start: 0.8685 (mtp) cc_final: 0.8438 (mtp) REVERT: K 599 ASP cc_start: 0.7583 (t0) cc_final: 0.7040 (t0) outliers start: 36 outliers final: 22 residues processed: 170 average time/residue: 0.1026 time to fit residues: 27.2899 Evaluate side-chains 164 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 583 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN H 81 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097872 restraints weight = 31129.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099943 restraints weight = 19202.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.101287 restraints weight = 14302.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.101796 restraints weight = 12129.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102482 restraints weight = 11212.409| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16722 Z= 0.154 Angle : 0.584 9.201 23857 Z= 0.328 Chirality : 0.036 0.246 2712 Planarity : 0.004 0.038 2012 Dihedral : 28.423 160.928 4559 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.11 % Allowed : 18.47 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1210 helix: 1.33 (0.20), residues: 731 sheet: -1.85 (0.84), residues: 41 loop : -2.24 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.031 0.002 TYR H 80 PHE 0.013 0.001 PHE K 375 TRP 0.021 0.001 TRP K 384 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00343 (16722) covalent geometry : angle 0.58435 (23857) hydrogen bonds : bond 0.04633 ( 824) hydrogen bonds : angle 2.88100 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8899 (p) cc_final: 0.8566 (t) REVERT: E 76 GLN cc_start: 0.8450 (pp30) cc_final: 0.7984 (tt0) REVERT: E 77 ASP cc_start: 0.8227 (m-30) cc_final: 0.7309 (t0) REVERT: F 25 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7507 (t0) REVERT: F 79 LYS cc_start: 0.9254 (mmmm) cc_final: 0.8887 (mmtm) REVERT: H 30 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7505 (ptp-170) REVERT: H 113 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8250 (mtmm) REVERT: K 350 LEU cc_start: 0.8719 (tp) cc_final: 0.8352 (tt) REVERT: K 384 TRP cc_start: 0.5819 (t60) cc_final: 0.5505 (t60) REVERT: K 527 MET cc_start: 0.8778 (mtp) cc_final: 0.8527 (mtp) REVERT: K 599 ASP cc_start: 0.7596 (t0) cc_final: 0.7079 (t0) outliers start: 22 outliers final: 18 residues processed: 164 average time/residue: 0.1066 time to fit residues: 26.8345 Evaluate side-chains 169 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 81 ASN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.132757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.093249 restraints weight = 30963.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095352 restraints weight = 18640.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096641 restraints weight = 13667.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097526 restraints weight = 11493.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097928 restraints weight = 10422.038| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16722 Z= 0.219 Angle : 0.639 11.798 23857 Z= 0.355 Chirality : 0.039 0.303 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.538 160.489 4559 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 2.87 % Allowed : 17.99 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1210 helix: 1.23 (0.20), residues: 726 sheet: -2.30 (0.74), residues: 49 loop : -2.33 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 77 TYR 0.039 0.002 TYR H 80 PHE 0.013 0.002 PHE K 375 TRP 0.019 0.001 TRP K 384 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00504 (16722) covalent geometry : angle 0.63945 (23857) hydrogen bonds : bond 0.05544 ( 824) hydrogen bonds : angle 3.16282 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8847 (p) REVERT: C 76 THR cc_start: 0.8904 (p) cc_final: 0.8563 (t) REVERT: E 76 GLN cc_start: 0.8491 (pp30) cc_final: 0.7996 (tt0) REVERT: E 77 ASP cc_start: 0.8260 (m-30) cc_final: 0.7311 (t0) REVERT: F 79 LYS cc_start: 0.9276 (mmmm) cc_final: 0.9008 (mmtm) REVERT: H 30 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7451 (ptp-170) REVERT: K 350 LEU cc_start: 0.8788 (tp) cc_final: 0.8410 (tt) REVERT: K 384 TRP cc_start: 0.5823 (t60) cc_final: 0.5522 (t60) REVERT: K 599 ASP cc_start: 0.7604 (t0) cc_final: 0.7089 (t0) outliers start: 30 outliers final: 26 residues processed: 166 average time/residue: 0.1099 time to fit residues: 28.0889 Evaluate side-chains 176 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 583 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 20 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 141 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN H 81 ASN K 258 ASN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.136019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097037 restraints weight = 30683.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.099244 restraints weight = 18096.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100685 restraints weight = 13132.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101533 restraints weight = 10932.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101534 restraints weight = 9917.129| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16722 Z= 0.141 Angle : 0.572 9.961 23857 Z= 0.321 Chirality : 0.036 0.273 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.353 160.494 4559 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 2.20 % Allowed : 18.66 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1210 helix: 1.59 (0.20), residues: 725 sheet: -1.77 (0.84), residues: 41 loop : -2.14 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.028 0.001 TYR H 80 PHE 0.015 0.001 PHE K 375 TRP 0.020 0.001 TRP K 384 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00308 (16722) covalent geometry : angle 0.57190 (23857) hydrogen bonds : bond 0.04346 ( 824) hydrogen bonds : angle 2.78403 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8910 (p) cc_final: 0.8581 (t) REVERT: E 76 GLN cc_start: 0.8545 (pp30) cc_final: 0.7996 (tt0) REVERT: E 77 ASP cc_start: 0.8307 (m-30) cc_final: 0.7336 (t0) REVERT: F 79 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8921 (mmtm) REVERT: H 30 ARG cc_start: 0.7804 (ptp90) cc_final: 0.7528 (ptp-170) REVERT: K 350 LEU cc_start: 0.8667 (tp) cc_final: 0.8294 (tt) REVERT: K 384 TRP cc_start: 0.5592 (t60) cc_final: 0.5324 (t60) REVERT: K 599 ASP cc_start: 0.7628 (t0) cc_final: 0.7123 (t0) outliers start: 23 outliers final: 21 residues processed: 168 average time/residue: 0.1046 time to fit residues: 27.4355 Evaluate side-chains 169 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 81 ASN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 329 ILE Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 TRP Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 103 optimal weight: 0.3980 chunk 136 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 81 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.132590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093062 restraints weight = 30925.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095125 restraints weight = 18750.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096433 restraints weight = 13794.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097257 restraints weight = 11585.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097574 restraints weight = 10550.156| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16722 Z= 0.227 Angle : 0.643 8.855 23857 Z= 0.356 Chirality : 0.039 0.314 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.520 159.882 4559 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.11 % Favored : 92.81 % Rotamer: Outliers : 2.78 % Allowed : 18.76 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1210 helix: 1.25 (0.20), residues: 727 sheet: -1.79 (0.83), residues: 41 loop : -2.26 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 92 TYR 0.037 0.002 TYR H 80 PHE 0.012 0.002 PHE K 375 TRP 0.017 0.001 TRP K 384 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00524 (16722) covalent geometry : angle 0.64283 (23857) hydrogen bonds : bond 0.05600 ( 824) hydrogen bonds : angle 3.19627 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.60 seconds wall clock time: 37 minutes 33.61 seconds (2253.61 seconds total)