Starting phenix.real_space_refine on Sat Sep 12 11:26:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k1p_9719/09_2026/6k1p_9719.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k1p_9719/09_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_9719/09_2026/6k1p_9719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k1p_9719/09_2026/6k1p_9719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k1p_9719/09_2026/6k1p_9719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k1p_9719/09_2026/6k1p_9719.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6k1p_9719/09_2026/6k1p_9719.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k1p_9719/09_2026/6k1p_9719.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.58, per 1000 atoms: 0.23 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: 1.39 Conformation dependent library (CDL) restraints added in 375.7 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: 1.99 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: 3.66 Time building geometry restraints manager: 1.81 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 1.435 1.508 -0.073 1.30e-02 5.92e+03 3.17e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.30e-02 5.92e+03 1.79e+01 ... (remaining 16717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 23710 4.26 - 8.52: 139 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=" O4' DG J 55 " pdb=" C4' DG J 55 " pdb=" C3' DG J 55 " ideal model delta sigma weight residual 106.00 102.49 3.51 6.00e-01 2.78e+00 3.43e+01 angle pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sigma weight residual 119.70 126.14 -6.44 1.20e+00 6.94e-01 2.88e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 123.09 -3.19 6.00e-01 2.78e+00 2.83e+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: 1964 0.065 - 0.129: 651 0.129 - 0.194: 79 0.194 - 0.258: 14 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.880 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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= 0.738 Angle : 1.136 21.289 23857 Z= 0.836 Chirality : 0.061 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/Z covalent geometry : bond 0.01047 / 0.74 (16722) covalent geometry : angle 1.13638 / 0.84 (23857) hydrogen bonds : bond 0.16283 / 11.20 ( 824) hydrogen bonds : angle 5.78747 / 4.11 ( 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 : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7971 (mmm) cc_final: 0.7770 (tpp) REVERT: B 88 TYR cc_start: 0.8660 (m-10) cc_final: 0.8229 (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: 0.7773 (m-10) REVERT: E 122 LYS cc_start: 0.8305 (pttt) cc_final: 0.8105 (pttp) REVERT: F 88 TYR cc_start: 0.8739 (m-10) cc_final: 0.7967 (m-80) REVERT: G 90 ASP cc_start: 0.8537 (t70) cc_final: 0.7581 (t0) REVERT: G 95 LYS cc_start: 0.8617 (tptm) cc_final: 0.8347 (mtpp) REVERT: H 80 TYR cc_start: 0.7648 (m-10) cc_final: 0.6916 (m-10) REVERT: K 350 LEU cc_start: 0.8984 (tp) cc_final: 0.8701 (tp) REVERT: K 351 ILE cc_start: 0.8521 (mt) cc_final: 0.8304 (pt) REVERT: K 362 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7230 (mt-10) REVERT: K 470 MET cc_start: 0.8401 (tpt) cc_final: 0.8088 (tpp) REVERT: K 511 LEU cc_start: 0.8520 (mt) cc_final: 0.8200 (tt) REVERT: K 527 MET cc_start: 0.7930 (mtm) cc_final: 0.7709 (mtp) REVERT: K 599 ASP cc_start: 0.7596 (t0) cc_final: 0.6923 (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: 0.1580 time to fit residues: 59.3863 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 : 0.355 ------------------------------------------------------------------------------- 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: 30.0000 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: 30.0000 chunk 122 optimal weight: 0.0050 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 2.0096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 125 GLN B 75 HIS B 93 GLN D 46 HIS E 68 GLN E 76 GLN G 38 ASN H 81 ASN K 205 ASN K 230 GLN K 357 GLN K 437 GLN K 477 ASN K 620 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099501 restraints weight = 31134.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100432 restraints weight = 17768.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100872 restraints weight = 14099.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100990 restraints weight = 12714.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101746 restraints weight = 12129.599| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16722 Z= 0.179 Angle : 0.737 8.465 23857 Z= 0.414 Chirality : 0.047 0.272 2712 Planarity : 0.006 0.073 2012 Dihedral : 29.604 168.049 4560 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.68 % Allowed : 10.14 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.23), residues: 1210 helix: -0.74 (0.18), residues: 723 sheet: -2.73 (0.70), residues: 55 loop : -2.97 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 655 TYR 0.024 0.002 TYR D 37 PHE 0.021 0.002 PHE K 375 TRP 0.019 0.002 TRP K 267 HIS 0.008 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (16722) covalent geometry : angle 0.73715 / 0.41 (23857) hydrogen bonds : bond 0.06816 / 4.66 ( 824) hydrogen bonds : angle 3.81380 / 2.64 ( 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 221 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8764 (m-80) cc_final: 0.8535 (m-80) REVERT: A 106 ASP cc_start: 0.8282 (m-30) cc_final: 0.8035 (m-30) REVERT: B 88 TYR cc_start: 0.8648 (m-10) cc_final: 0.8435 (m-80) REVERT: D 102 GLU cc_start: 0.6713 (tp30) cc_final: 0.6399 (tm-30) REVERT: E 118 THR cc_start: 0.9516 (m) cc_final: 0.9136 (p) REVERT: E 122 LYS cc_start: 0.8299 (pttt) cc_final: 0.8061 (pttp) REVERT: F 88 TYR cc_start: 0.8851 (m-10) cc_final: 0.8642 (m-80) REVERT: G 95 LYS cc_start: 0.8599 (tptm) cc_final: 0.8316 (mtpp) REVERT: H 30 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7361 (ptp-170) REVERT: K 219 LEU cc_start: 0.8141 (tt) cc_final: 0.7920 (tt) REVERT: K 324 ASP cc_start: 0.7886 (t70) cc_final: 0.7668 (t0) REVERT: K 350 LEU cc_start: 0.8876 (tp) cc_final: 0.8387 (tt) REVERT: K 351 ILE cc_start: 0.8544 (mt) cc_final: 0.8182 (mt) REVERT: K 357 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: K 440 TRP cc_start: 0.7195 (m100) cc_final: 0.6973 (m100) REVERT: K 470 MET cc_start: 0.8148 (tpt) cc_final: 0.7857 (tpp) REVERT: K 599 ASP cc_start: 0.7398 (t0) cc_final: 0.6779 (t0) REVERT: K 638 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6782 (tt0) outliers start: 28 outliers final: 15 residues processed: 206 average time/residue: 0.1223 time to fit residues: 37.3804 Evaluate side-chains 183 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 222 GLU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 357 GLN Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 379 GLN Chi-restraints excluded: chain K residue 532 ASP Chi-restraints excluded: chain K residue 534 LEU Chi-restraints excluded: chain K residue 638 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 34 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 40.0000 chunk 139 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 75 HIS D 81 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 230 GLN ** K 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 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 = 0.3887 r_free = 0.3887 target = 0.137609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102088 restraints weight = 31918.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103111 restraints weight = 25209.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103068 restraints weight = 22798.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103511 restraints weight = 19432.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103581 restraints weight = 18366.701| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 16722 Z= 0.259 Angle : 0.789 8.581 23857 Z= 0.431 Chirality : 0.050 0.322 2712 Planarity : 0.006 0.084 2012 Dihedral : 29.545 165.102 4559 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.10 % Favored : 91.82 % Rotamer: Outliers : 3.06 % Allowed : 11.29 % Favored : 85.65 % 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: -1.87 (0.24), residues: 1210 helix: -0.12 (0.19), residues: 722 sheet: -2.69 (0.69), residues: 55 loop : -2.99 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 655 TYR 0.019 0.002 TYR C 57 PHE 0.016 0.002 PHE K 375 TRP 0.011 0.001 TRP K 267 HIS 0.007 0.002 HIS K 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.26 (16722) covalent geometry : angle 0.78864 / 0.43 (23857) hydrogen bonds : bond 0.07193 / 4.86 ( 824) hydrogen bonds : angle 3.81047 / 2.64 ( 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 194 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.9208 (tptt) cc_final: 0.8986 (tttp) REVERT: E 77 ASP cc_start: 0.8404 (m-30) cc_final: 0.7086 (t0) REVERT: E 122 LYS cc_start: 0.8300 (pttt) cc_final: 0.8081 (pttp) REVERT: G 95 LYS cc_start: 0.8670 (tptm) cc_final: 0.8420 (mtpp) REVERT: H 30 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7368 (ptp-170) REVERT: H 80 TYR cc_start: 0.7488 (m-10) cc_final: 0.7172 (m-10) REVERT: H 113 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8171 (mtmm) REVERT: K 241 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7067 (mp) REVERT: K 276 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8370 (tt) REVERT: K 350 LEU cc_start: 0.8888 (tp) cc_final: 0.8595 (tt) REVERT: K 470 MET cc_start: 0.8278 (tpt) cc_final: 0.8030 (tpp) REVERT: K 599 ASP cc_start: 0.7375 (t0) cc_final: 0.6788 (t0) outliers start: 32 outliers final: 20 residues processed: 175 average time/residue: 0.1085 time to fit residues: 28.8628 Evaluate side-chains 173 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE 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 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU 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 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 241 ILE 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 534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 96 optimal weight: 30.0000 chunk 94 optimal weight: 30.0000 chunk 101 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN F 25 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 = 0.3941 r_free = 0.3941 target = 0.141586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.105576 restraints weight = 31393.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108153 restraints weight = 22471.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108318 restraints weight = 14460.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108675 restraints weight = 13411.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108690 restraints weight = 12556.746| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16722 Z= 0.139 Angle : 0.641 9.748 23857 Z= 0.365 Chirality : 0.044 0.306 2712 Planarity : 0.004 0.053 2012 Dihedral : 29.325 165.363 4559 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.79 % Favored : 94.13 % Rotamer: Outliers : 2.39 % Allowed : 13.11 % Favored : 84.50 % 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: -0.99 (0.25), residues: 1210 helix: 0.60 (0.20), residues: 719 sheet: -2.42 (0.71), residues: 55 loop : -2.58 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 67 TYR 0.031 0.002 TYR D 37 PHE 0.021 0.001 PHE K 375 TRP 0.012 0.001 TRP K 384 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (16722) covalent geometry : angle 0.64120 / 0.37 (23857) hydrogen bonds : bond 0.05335 / 3.64 ( 824) hydrogen bonds : angle 3.19139 / 2.21 ( 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 201 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8909 (tm130) cc_final: 0.8621 (tm-30) REVERT: E 77 ASP cc_start: 0.8026 (m-30) cc_final: 0.7041 (t0) REVERT: G 95 LYS cc_start: 0.8604 (tptm) cc_final: 0.8367 (mtpp) REVERT: H 30 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7283 (ptp-170) REVERT: H 113 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8220 (mtmm) REVERT: K 210 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7648 (tp) REVERT: K 276 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8340 (tt) REVERT: K 350 LEU cc_start: 0.8906 (tp) cc_final: 0.8611 (tt) REVERT: K 599 ASP cc_start: 0.7394 (t0) cc_final: 0.6833 (t0) outliers start: 25 outliers final: 14 residues processed: 188 average time/residue: 0.1179 time to fit residues: 33.1629 Evaluate side-chains 171 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE 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 G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 210 LEU 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 379 GLN Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 109 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 108 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 526 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.140852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105241 restraints weight = 31530.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106479 restraints weight = 24434.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106745 restraints weight = 18718.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107125 restraints weight = 17492.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107253 restraints weight = 15796.217| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16722 Z= 0.144 Angle : 0.633 8.095 23857 Z= 0.358 Chirality : 0.044 0.305 2712 Planarity : 0.004 0.044 2012 Dihedral : 29.283 165.194 4559 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 2.30 % Allowed : 13.68 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1210 helix: 0.80 (0.20), residues: 719 sheet: -2.38 (0.70), residues: 55 loop : -2.46 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 411 TYR 0.033 0.002 TYR H 80 PHE 0.020 0.001 PHE K 375 TRP 0.008 0.001 TRP K 384 HIS 0.003 0.001 HIS K 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (16722) covalent geometry : angle 0.63294 / 0.36 (23857) hydrogen bonds : bond 0.05336 / 3.62 ( 824) hydrogen bonds : angle 3.15763 / 2.18 ( 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 184 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8929 (p) REVERT: E 77 ASP cc_start: 0.7909 (m-30) cc_final: 0.7025 (t0) REVERT: G 95 LYS cc_start: 0.8641 (tptm) cc_final: 0.8391 (mtpp) REVERT: H 30 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7394 (ptp-170) REVERT: H 113 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8143 (mtmm) REVERT: K 276 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8356 (tt) REVERT: K 350 LEU cc_start: 0.8895 (tp) cc_final: 0.8640 (tt) REVERT: K 599 ASP cc_start: 0.7405 (t0) cc_final: 0.6859 (t0) outliers start: 24 outliers final: 14 residues processed: 172 average time/residue: 0.1195 time to fit residues: 30.8971 Evaluate side-chains 163 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR 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 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 417 VAL Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN F 25 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.140997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104445 restraints weight = 31702.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106954 restraints weight = 23673.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107146 restraints weight = 16319.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107256 restraints weight = 14671.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107291 restraints weight = 14301.021| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16722 Z= 0.152 Angle : 0.632 8.083 23857 Z= 0.355 Chirality : 0.043 0.308 2712 Planarity : 0.004 0.041 2012 Dihedral : 29.215 165.524 4559 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 2.87 % Allowed : 15.22 % Favored : 81.91 % 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: -0.59 (0.25), residues: 1210 helix: 0.87 (0.20), residues: 735 sheet: -2.29 (0.70), residues: 55 loop : -2.46 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 547 TYR 0.034 0.002 TYR H 80 PHE 0.021 0.001 PHE K 375 TRP 0.009 0.001 TRP K 384 HIS 0.004 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (16722) covalent geometry : angle 0.63201 / 0.36 (23857) hydrogen bonds : bond 0.05315 / 3.61 ( 824) hydrogen bonds : angle 3.09692 / 2.13 ( 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 185 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 84 GLN cc_start: 0.9436 (tp40) cc_final: 0.9114 (tp40) REVERT: E 77 ASP cc_start: 0.7898 (m-30) cc_final: 0.7120 (t0) REVERT: F 79 LYS cc_start: 0.9326 (mmmt) cc_final: 0.9124 (mmtm) REVERT: G 95 LYS cc_start: 0.8644 (tptm) cc_final: 0.8427 (mtpp) REVERT: H 30 ARG cc_start: 0.7793 (ptp90) cc_final: 0.7415 (ptp-170) REVERT: H 113 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: K 210 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7761 (tp) REVERT: K 276 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8537 (tt) REVERT: K 335 MET cc_start: 0.8494 (tpp) cc_final: 0.7850 (tpp) REVERT: K 350 LEU cc_start: 0.8895 (tp) cc_final: 0.8643 (tt) REVERT: K 599 ASP cc_start: 0.7428 (t0) cc_final: 0.6919 (t0) outliers start: 30 outliers final: 20 residues processed: 173 average time/residue: 0.1186 time to fit residues: 30.8636 Evaluate side-chains 173 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE 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 112 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 210 LEU 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 417 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 118 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 99 optimal weight: 40.0000 chunk 26 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN C 84 GLN ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 601 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 = 0.3876 r_free = 0.3876 target = 0.136537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.098881 restraints weight = 31434.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101218 restraints weight = 22427.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.101509 restraints weight = 15458.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.101804 restraints weight = 14032.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101735 restraints weight = 13090.467| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16722 Z= 0.300 Angle : 0.789 9.761 23857 Z= 0.426 Chirality : 0.050 0.331 2712 Planarity : 0.006 0.043 2012 Dihedral : 29.339 164.379 4559 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 4.02 % Allowed : 14.45 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.24), residues: 1210 helix: 0.52 (0.19), residues: 731 sheet: -2.40 (0.75), residues: 48 loop : -2.75 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.058 0.003 TYR H 80 PHE 0.019 0.002 PHE K 375 TRP 0.006 0.001 TRP K 600 HIS 0.006 0.002 HIS K 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.30 (16722) covalent geometry : angle 0.78948 / 0.43 (23857) hydrogen bonds : bond 0.07042 / 4.73 ( 824) hydrogen bonds : angle 3.68374 / 2.53 ( 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: 42 poor density : 143 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8373 (mm) REVERT: D 102 GLU cc_start: 0.6356 (tp30) cc_final: 0.6128 (tp30) REVERT: E 77 ASP cc_start: 0.7960 (m-30) cc_final: 0.7194 (t0) REVERT: F 58 LEU cc_start: 0.8909 (tp) cc_final: 0.8628 (tp) REVERT: G 95 LYS cc_start: 0.8697 (tptm) cc_final: 0.8449 (mtpp) REVERT: H 30 ARG cc_start: 0.7763 (ptp90) cc_final: 0.7322 (ptp-170) REVERT: H 113 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8130 (mtmm) REVERT: K 210 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7973 (tp) REVERT: K 276 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8646 (tt) REVERT: K 335 MET cc_start: 0.8543 (tpp) cc_final: 0.7909 (tpp) REVERT: K 350 LEU cc_start: 0.8850 (tp) cc_final: 0.8577 (tt) REVERT: K 599 ASP cc_start: 0.7551 (t0) cc_final: 0.7046 (t0) outliers start: 42 outliers final: 26 residues processed: 169 average time/residue: 0.1146 time to fit residues: 30.0404 Evaluate side-chains 166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 352 THR Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 379 GLN Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 521 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 75 HIS B 93 GLN F 25 ASN K 586 ASN ** 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 = 0.3929 r_free = 0.3929 target = 0.140432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103509 restraints weight = 31674.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106007 restraints weight = 22268.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106225 restraints weight = 14070.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.106366 restraints weight = 14062.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106453 restraints weight = 13224.463| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16722 Z= 0.144 Angle : 0.636 13.487 23857 Z= 0.357 Chirality : 0.044 0.316 2712 Planarity : 0.004 0.041 2012 Dihedral : 29.120 165.404 4559 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 2.11 % Allowed : 16.56 % Favored : 81.34 % 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: -0.50 (0.25), residues: 1210 helix: 0.97 (0.20), residues: 731 sheet: -2.20 (0.72), residues: 55 loop : -2.43 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 89 TYR 0.030 0.002 TYR H 80 PHE 0.020 0.001 PHE K 375 TRP 0.010 0.001 TRP K 384 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (16722) covalent geometry : angle 0.63554 / 0.36 (23857) hydrogen bonds : bond 0.05382 / 3.66 ( 824) hydrogen bonds : angle 3.13113 / 2.13 ( 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 171 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 SER cc_start: 0.8574 (m) cc_final: 0.8329 (t) REVERT: E 77 ASP cc_start: 0.7795 (m-30) cc_final: 0.7220 (t0) REVERT: G 95 LYS cc_start: 0.8621 (tptm) cc_final: 0.8408 (mtpp) REVERT: H 30 ARG cc_start: 0.7757 (ptp90) cc_final: 0.7410 (ptp-170) REVERT: H 113 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8216 (mtmm) REVERT: K 210 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7843 (tp) REVERT: K 276 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8641 (tt) REVERT: K 335 MET cc_start: 0.8409 (tpp) cc_final: 0.7826 (tpp) REVERT: K 350 LEU cc_start: 0.8886 (tp) cc_final: 0.8596 (tt) REVERT: K 599 ASP cc_start: 0.7456 (t0) cc_final: 0.6930 (t0) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 0.1122 time to fit residues: 28.0379 Evaluate side-chains 158 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 292 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 534 LEU Chi-restraints excluded: chain K residue 551 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 40.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN 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 = 0.3900 r_free = 0.3900 target = 0.138215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101237 restraints weight = 31731.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.103122 restraints weight = 25263.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103416 restraints weight = 18341.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.103607 restraints weight = 17052.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.103665 restraints weight = 15616.426| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16722 Z= 0.229 Angle : 0.707 8.621 23857 Z= 0.387 Chirality : 0.046 0.327 2712 Planarity : 0.005 0.042 2012 Dihedral : 29.169 164.680 4559 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.15 % Rotamer: Outliers : 2.49 % Allowed : 16.94 % 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: -0.69 (0.25), residues: 1210 helix: 0.84 (0.20), residues: 728 sheet: -2.58 (0.74), residues: 50 loop : -2.52 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.044 0.002 TYR H 80 PHE 0.017 0.002 PHE K 375 TRP 0.006 0.001 TRP K 384 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.23 (16722) covalent geometry : angle 0.70710 / 0.39 (23857) hydrogen bonds : bond 0.06202 / 4.19 ( 824) hydrogen bonds : angle 3.40238 / 2.32 ( 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 161 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8471 (mm) REVERT: E 77 ASP cc_start: 0.7770 (m-30) cc_final: 0.7231 (t0) REVERT: G 95 LYS cc_start: 0.8677 (tptm) cc_final: 0.8448 (mtpp) REVERT: H 30 ARG cc_start: 0.7705 (ptp90) cc_final: 0.7331 (ptp-170) REVERT: H 113 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: K 210 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7988 (tp) REVERT: K 276 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8717 (tt) REVERT: K 335 MET cc_start: 0.8377 (tpp) cc_final: 0.7836 (tpp) REVERT: K 350 LEU cc_start: 0.8845 (tp) cc_final: 0.8574 (tt) REVERT: K 599 ASP cc_start: 0.7479 (t0) cc_final: 0.6960 (t0) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.1059 time to fit residues: 25.0061 Evaluate side-chains 154 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR 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 210 LEU 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 363 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 20 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 chunk 128 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.141565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.105590 restraints weight = 31513.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106925 restraints weight = 22296.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107062 restraints weight = 17641.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.107439 restraints weight = 16373.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107547 restraints weight = 14514.825| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16722 Z= 0.131 Angle : 0.618 9.184 23857 Z= 0.349 Chirality : 0.042 0.319 2712 Planarity : 0.004 0.041 2012 Dihedral : 28.996 165.581 4559 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.20 % Allowed : 17.32 % Favored : 80.48 % 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: -0.28 (0.25), residues: 1210 helix: 1.13 (0.20), residues: 733 sheet: -2.55 (0.73), residues: 50 loop : -2.29 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.034 0.002 TYR H 80 PHE 0.019 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/Z covalent geometry : bond 0.00229 / 0.13 (16722) covalent geometry : angle 0.61755 / 0.35 (23857) hydrogen bonds : bond 0.05030 / 3.42 ( 824) hydrogen bonds : angle 3.00735 / 2.05 ( 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 172 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 THR cc_start: 0.8800 (p) cc_final: 0.8455 (t) REVERT: E 77 ASP cc_start: 0.7790 (m-30) cc_final: 0.7239 (t0) REVERT: G 95 LYS cc_start: 0.8664 (tptm) cc_final: 0.8422 (mtpp) REVERT: H 30 ARG cc_start: 0.7819 (ptp90) cc_final: 0.7472 (ptp-170) REVERT: H 113 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8223 (mtmm) REVERT: K 225 LEU cc_start: 0.8392 (mm) cc_final: 0.8177 (mm) REVERT: K 276 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8702 (tt) REVERT: K 335 MET cc_start: 0.8371 (tpp) cc_final: 0.7820 (tpp) REVERT: K 350 LEU cc_start: 0.8845 (tp) cc_final: 0.8575 (tt) REVERT: K 599 ASP cc_start: 0.7544 (t0) cc_final: 0.7020 (t0) outliers start: 23 outliers final: 13 residues processed: 161 average time/residue: 0.1151 time to fit residues: 28.1365 Evaluate side-chains 160 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 77 LEU 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 82 THR 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 223 MET Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 507 LEU Chi-restraints excluded: chain K residue 521 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 103 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 137 optimal weight: 7.9990 chunk 26 optimal weight: 0.0050 chunk 97 optimal weight: 30.0000 chunk 40 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.141647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105896 restraints weight = 31514.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107099 restraints weight = 23237.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107245 restraints weight = 18174.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107679 restraints weight = 17141.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107709 restraints weight = 15197.849| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 16722 Z= 0.144 Angle : 0.783 59.199 23857 Z= 0.453 Chirality : 0.042 0.318 2712 Planarity : 0.004 0.041 2012 Dihedral : 28.996 165.542 4559 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 1.63 % Allowed : 18.09 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.24 (0.25), residues: 1210 helix: 1.17 (0.20), residues: 733 sheet: -2.54 (0.72), residues: 50 loop : -2.27 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 92 TYR 0.032 0.002 TYR H 80 PHE 0.019 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/Z covalent geometry : bond 0.00274 / 0.14 (16722) covalent geometry : angle 0.78275 / 0.45 (23857) hydrogen bonds : bond 0.05040 / 3.43 ( 824) hydrogen bonds : angle 3.03069 / 2.06 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.13 seconds wall clock time: 35 minutes 24.98 seconds (2124.98 seconds total)