Starting phenix.real_space_refine on Fri Jul 3 20:16:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnt_61626/07_2026/9jnt_61626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnt_61626/07_2026/9jnt_61626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnt_61626/07_2026/9jnt_61626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnt_61626/07_2026/9jnt_61626.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnt_61626/07_2026/9jnt_61626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnt_61626/07_2026/9jnt_61626.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9366 2.51 5 N 2985 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16283 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: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4240 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 496} Chain breaks: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.63, per 1000 atoms: 0.22 Number of scatterers: 16283 At special positions: 0 Unit cell: (93.095, 116.91, 158.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 O 3612 8.00 N 2985 7.00 C 9366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 576.0 milliseconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 63.5% alpha, 3.6% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.643A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.605A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.843A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.599A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.465A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.504A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.539A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.606A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.032A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.557A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.512A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.133A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.857A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.519A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 115 No H-bonds generated for 'chain 'K' and resid 114 through 115' Processing helix chain 'K' and resid 116 through 119 removed outlier: 3.560A pdb=" N PHE K 119 " --> pdb=" O SER K 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 120 through 129 removed outlier: 4.279A pdb=" N ALA K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 136 removed outlier: 4.089A pdb=" N GLN K 135 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 136 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 4.228A pdb=" N GLU K 263 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 removed outlier: 3.684A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 343 removed outlier: 3.583A pdb=" N PHE K 343 " --> pdb=" O VAL K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 377 through 385 Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 476 removed outlier: 3.764A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 482 Processing helix chain 'K' and resid 494 through 498 removed outlier: 3.583A pdb=" N LEU K 497 " --> pdb=" O ASP K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.550A pdb=" N GLN K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.840A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.065A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG K 611 " --> pdb=" O GLN K 607 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.770A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 3.803A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.001A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.958A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.814A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.976A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 301 through 302 removed outlier: 7.579A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 427 through 431 556 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2188 1.32 - 1.44: 5908 1.44 - 1.57: 8450 1.57 - 1.69: 586 1.69 - 1.81: 43 Bond restraints: 17175 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.34e-02 5.57e+03 2.57e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.29e-02 6.01e+03 9.38e+00 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.93e+00 bond pdb=" C3' DC J 72 " pdb=" C2' DC J 72 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DA I 60 " pdb=" O3' DA I 60 " ideal model delta sigma weight residual 1.435 1.398 0.037 1.30e-02 5.92e+03 8.25e+00 ... (remaining 17170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 22799 1.54 - 3.07: 1488 3.07 - 4.61: 142 4.61 - 6.14: 26 6.14 - 7.68: 7 Bond angle restraints: 24462 Sorted by residual: angle pdb=" O4' DG J 53 " pdb=" C4' DG J 53 " pdb=" C3' DG J 53 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.61e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I 134 " pdb=" C4 DT I 134 " pdb=" O4 DT I 134 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DG J 4 " pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " ideal model delta sigma weight residual 106.00 103.34 2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J 105 " pdb=" C4 DT J 105 " pdb=" O4 DT J 105 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 24457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 8160 35.90 - 71.81: 1409 71.81 - 107.71: 19 107.71 - 143.61: 3 143.61 - 179.52: 11 Dihedral angle restraints: 9602 sinusoidal: 5855 harmonic: 3747 Sorted by residual: dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 149.22 30.78 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual -180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA HIS B 18 " pdb=" C HIS B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 9599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2063 0.050 - 0.100: 581 0.100 - 0.150: 124 0.150 - 0.200: 8 0.200 - 0.251: 2 Chirality restraints: 2778 Sorted by residual: chirality pdb=" CA LEU K 421 " pdb=" N LEU K 421 " pdb=" C LEU K 421 " pdb=" CB LEU K 421 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C3' DC I 110 " pdb=" C4' DC I 110 " pdb=" O3' DC I 110 " pdb=" C2' DC I 110 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C3' DA I 20 " pdb=" C4' DA I 20 " pdb=" O3' DA I 20 " pdb=" C2' DA I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.09e-01 ... (remaining 2775 not shown) Planarity restraints: 2087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO K 189 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 417 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C VAL K 417 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL K 417 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU K 418 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO K 489 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.029 5.00e-02 4.00e+02 ... (remaining 2084 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 118 2.57 - 3.15: 12519 3.15 - 3.73: 28110 3.73 - 4.32: 39262 4.32 - 4.90: 58382 Nonbonded interactions: 138391 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.985 2.170 nonbonded pdb=" O PRO K 372 " pdb=" OG SER K 376 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.165 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 2.190 3.040 nonbonded pdb=" O VAL K 398 " pdb=" ND1 HIS K 402 " model vdw 2.200 3.120 ... (remaining 138386 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.490 Find NCS groups from input model: 0.160 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 17175 Z= 0.498 Angle : 0.787 7.680 24462 Z= 0.642 Chirality : 0.047 0.251 2778 Planarity : 0.005 0.111 2087 Dihedral : 26.481 179.516 7174 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.16 (0.25), residues: 1259 helix: 1.27 (0.19), residues: 768 sheet: -2.43 (0.66), residues: 62 loop : -1.63 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 52 TYR 0.016 0.001 TYR K 320 PHE 0.033 0.002 PHE K 381 TRP 0.018 0.002 TRP K 364 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.50 (17175) covalent geometry : angle 0.78665 / 0.64 (24462) hydrogen bonds : bond 0.08890 / 6.08 ( 926) hydrogen bonds : angle 4.10263 / 2.93 ( 2378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8898 (pm20) cc_final: 0.8625 (pm20) REVERT: C 104 GLN cc_start: 0.8354 (mm110) cc_final: 0.7799 (mm110) REVERT: D 43 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8911 (mmtt) REVERT: D 90 GLU cc_start: 0.8759 (mp0) cc_final: 0.8406 (mp0) REVERT: E 59 GLU cc_start: 0.8313 (pm20) cc_final: 0.8103 (pm20) REVERT: E 77 ASP cc_start: 0.8668 (m-30) cc_final: 0.8397 (m-30) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7948 (m-30) REVERT: G 75 LYS cc_start: 0.8801 (mttm) cc_final: 0.8487 (mmmt) REVERT: H 65 ASP cc_start: 0.8628 (t70) cc_final: 0.8052 (t0) REVERT: K 184 GLN cc_start: 0.8499 (pm20) cc_final: 0.8281 (mp10) REVERT: K 294 CYS cc_start: 0.8331 (m) cc_final: 0.7606 (t) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.8034 time to fit residues: 180.1659 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 93 GLN G 73 ASN K 86 ASN K 111 HIS K 361 HIS K 617 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.058685 restraints weight = 37403.720| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.32 r_work: 0.2753 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17175 Z= 0.283 Angle : 0.757 8.762 24462 Z= 0.409 Chirality : 0.051 0.421 2778 Planarity : 0.005 0.057 2087 Dihedral : 30.723 178.501 4613 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.37 % Allowed : 11.14 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.22 (0.24), residues: 1259 helix: 1.34 (0.19), residues: 776 sheet: -2.17 (0.66), residues: 71 loop : -1.73 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 186 TYR 0.013 0.002 TYR H 34 PHE 0.016 0.002 PHE K 381 TRP 0.016 0.001 TRP K 364 HIS 0.007 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.28 (17175) covalent geometry : angle 0.75728 / 0.41 (24462) hydrogen bonds : bond 0.05509 / 3.53 ( 926) hydrogen bonds : angle 3.67179 / 2.63 ( 2378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7531 (p-80) REVERT: A 59 GLU cc_start: 0.8866 (pm20) cc_final: 0.8407 (pm20) REVERT: A 81 ASP cc_start: 0.8714 (t0) cc_final: 0.8488 (t0) REVERT: E 59 GLU cc_start: 0.8389 (pm20) cc_final: 0.7845 (pm20) REVERT: E 77 ASP cc_start: 0.9017 (m-30) cc_final: 0.8738 (m-30) REVERT: E 105 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: E 123 ASP cc_start: 0.9106 (m-30) cc_final: 0.8852 (m-30) REVERT: G 64 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: H 65 ASP cc_start: 0.8745 (t70) cc_final: 0.8200 (t0) REVERT: K 184 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: K 294 CYS cc_start: 0.8140 (m) cc_final: 0.7277 (t) REVERT: K 385 PHE cc_start: 0.7310 (t80) cc_final: 0.6927 (t80) REVERT: K 568 ASP cc_start: 0.8477 (p0) cc_final: 0.8260 (p0) REVERT: K 655 ARG cc_start: 0.8423 (pmt-80) cc_final: 0.8184 (pmt-80) outliers start: 26 outliers final: 12 residues processed: 175 average time/residue: 0.7578 time to fit residues: 143.1478 Evaluate side-chains 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS C 73 ASN E 68 GLN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.059896 restraints weight = 37700.443| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.31 r_work: 0.2805 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17175 Z= 0.148 Angle : 0.692 10.876 24462 Z= 0.380 Chirality : 0.047 0.378 2778 Planarity : 0.005 0.053 2087 Dihedral : 30.650 178.188 4613 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.92 % Allowed : 14.06 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.41 (0.25), residues: 1259 helix: 1.49 (0.19), residues: 776 sheet: -2.08 (0.67), residues: 71 loop : -1.67 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.011 0.001 TYR H 34 PHE 0.012 0.001 PHE K 381 TRP 0.017 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (17175) covalent geometry : angle 0.69223 / 0.38 (24462) hydrogen bonds : bond 0.04574 / 2.91 ( 926) hydrogen bonds : angle 3.45321 / 2.47 ( 2378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8398 (pm20) REVERT: A 79 LYS cc_start: 0.8840 (tttp) cc_final: 0.8498 (tttp) REVERT: E 59 GLU cc_start: 0.8407 (pm20) cc_final: 0.7888 (pm20) REVERT: E 77 ASP cc_start: 0.9023 (m-30) cc_final: 0.8741 (m-30) REVERT: E 105 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: E 123 ASP cc_start: 0.9104 (m-30) cc_final: 0.8881 (m-30) REVERT: G 64 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: G 101 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8610 (p) REVERT: H 65 ASP cc_start: 0.8744 (t70) cc_final: 0.8198 (t0) REVERT: H 102 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8663 (tm-30) REVERT: K 294 CYS cc_start: 0.8076 (m) cc_final: 0.7229 (t) REVERT: K 568 ASP cc_start: 0.8355 (p0) cc_final: 0.8025 (p0) REVERT: K 586 ASN cc_start: 0.9076 (t0) cc_final: 0.8862 (t0) REVERT: K 655 ARG cc_start: 0.8373 (pmt-80) cc_final: 0.8120 (pmt-80) outliers start: 21 outliers final: 12 residues processed: 183 average time/residue: 0.7749 time to fit residues: 152.9154 Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 232 ILE Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 80 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 93 GLN G 73 ASN G 104 GLN K 317 ASN K 505 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060544 restraints weight = 37559.166| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.31 r_work: 0.2812 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17175 Z= 0.159 Angle : 0.669 8.145 24462 Z= 0.369 Chirality : 0.046 0.334 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.527 179.287 4613 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.01 % Allowed : 15.07 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.58 (0.25), residues: 1259 helix: 1.63 (0.19), residues: 776 sheet: -1.97 (0.68), residues: 69 loop : -1.65 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 95 TYR 0.012 0.001 TYR A 41 PHE 0.010 0.001 PHE K 381 TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (17175) covalent geometry : angle 0.66920 / 0.37 (24462) hydrogen bonds : bond 0.04424 / 2.83 ( 926) hydrogen bonds : angle 3.31217 / 2.36 ( 2378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8875 (pm20) cc_final: 0.8450 (pm20) REVERT: E 59 GLU cc_start: 0.8469 (pm20) cc_final: 0.7925 (pm20) REVERT: E 77 ASP cc_start: 0.9008 (m-30) cc_final: 0.8729 (m-30) REVERT: E 123 ASP cc_start: 0.9095 (m-30) cc_final: 0.8872 (m-30) REVERT: F 85 ASP cc_start: 0.8844 (m-30) cc_final: 0.8548 (m-30) REVERT: G 64 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: G 73 ASN cc_start: 0.8333 (m-40) cc_final: 0.7626 (t0) REVERT: H 65 ASP cc_start: 0.8734 (t70) cc_final: 0.8158 (t0) REVERT: H 73 GLU cc_start: 0.9003 (tp30) cc_final: 0.8784 (mm-30) REVERT: H 102 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8570 (tm-30) REVERT: K 196 LEU cc_start: 0.8950 (tt) cc_final: 0.8695 (tt) REVERT: K 294 CYS cc_start: 0.8109 (m) cc_final: 0.7207 (t) REVERT: K 385 PHE cc_start: 0.6838 (t80) cc_final: 0.6304 (t80) REVERT: K 568 ASP cc_start: 0.8298 (p0) cc_final: 0.8029 (p0) REVERT: K 586 ASN cc_start: 0.9091 (t0) cc_final: 0.8854 (t0) outliers start: 33 outliers final: 19 residues processed: 184 average time/residue: 0.7632 time to fit residues: 151.9924 Evaluate side-chains 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 72 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.087676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.057557 restraints weight = 37400.991| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.35 r_work: 0.2734 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 17175 Z= 0.346 Angle : 0.778 9.437 24462 Z= 0.415 Chirality : 0.052 0.362 2778 Planarity : 0.005 0.056 2087 Dihedral : 30.819 179.086 4613 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.83 % Allowed : 16.99 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 (0.24), residues: 1259 helix: 1.35 (0.19), residues: 777 sheet: -2.18 (0.67), residues: 69 loop : -1.73 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.017 0.002 TYR H 34 PHE 0.011 0.002 PHE K 381 TRP 0.012 0.001 TRP K 364 HIS 0.008 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.35 (17175) covalent geometry : angle 0.77786 / 0.41 (24462) hydrogen bonds : bond 0.06012 / 3.85 ( 926) hydrogen bonds : angle 3.53851 / 2.54 ( 2378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8883 (pm20) cc_final: 0.8374 (pm20) REVERT: B 24 ASP cc_start: 0.8471 (t0) cc_final: 0.8235 (t0) REVERT: C 90 ASP cc_start: 0.8352 (t0) cc_final: 0.8003 (t0) REVERT: D 68 GLU cc_start: 0.8412 (pt0) cc_final: 0.8154 (tp30) REVERT: E 59 GLU cc_start: 0.8460 (pm20) cc_final: 0.7847 (pm20) REVERT: E 77 ASP cc_start: 0.9019 (m-30) cc_final: 0.8748 (m-30) REVERT: E 123 ASP cc_start: 0.9099 (m-30) cc_final: 0.8837 (m-30) REVERT: G 64 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: H 65 ASP cc_start: 0.8807 (t70) cc_final: 0.8269 (t0) REVERT: H 102 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8474 (tm-30) REVERT: K 196 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8703 (tt) REVERT: K 263 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.9011 (mp0) REVERT: K 294 CYS cc_start: 0.8267 (m) cc_final: 0.7318 (t) REVERT: K 568 ASP cc_start: 0.8302 (p0) cc_final: 0.8044 (p0) REVERT: K 586 ASN cc_start: 0.9146 (t0) cc_final: 0.8915 (t0) outliers start: 31 outliers final: 20 residues processed: 171 average time/residue: 0.7477 time to fit residues: 138.0858 Evaluate side-chains 175 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 9 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059392 restraints weight = 37532.994| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.30 r_work: 0.2764 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17175 Z= 0.162 Angle : 0.694 9.413 24462 Z= 0.377 Chirality : 0.047 0.316 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.756 178.926 4613 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 17.35 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.45 (0.25), residues: 1259 helix: 1.53 (0.19), residues: 776 sheet: -2.13 (0.67), residues: 69 loop : -1.68 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.012 0.001 TYR H 34 PHE 0.012 0.001 PHE A 78 TRP 0.017 0.001 TRP K 364 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (17175) covalent geometry : angle 0.69423 / 0.38 (24462) hydrogen bonds : bond 0.04763 / 3.02 ( 926) hydrogen bonds : angle 3.36368 / 2.41 ( 2378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8849 (pm20) cc_final: 0.8321 (pm20) REVERT: B 24 ASP cc_start: 0.8409 (t0) cc_final: 0.8165 (t0) REVERT: C 90 ASP cc_start: 0.8243 (t0) cc_final: 0.7948 (t0) REVERT: D 68 GLU cc_start: 0.8396 (pt0) cc_final: 0.8145 (tp30) REVERT: E 59 GLU cc_start: 0.8444 (pm20) cc_final: 0.7823 (pm20) REVERT: E 77 ASP cc_start: 0.9025 (m-30) cc_final: 0.8753 (m-30) REVERT: E 123 ASP cc_start: 0.9107 (m-30) cc_final: 0.8890 (m-30) REVERT: G 64 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: G 73 ASN cc_start: 0.8447 (m-40) cc_final: 0.7694 (t0) REVERT: H 65 ASP cc_start: 0.8759 (t70) cc_final: 0.8228 (t0) REVERT: H 102 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8491 (tm-30) REVERT: K 196 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8679 (tt) REVERT: K 263 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8919 (mp0) REVERT: K 294 CYS cc_start: 0.8220 (m) cc_final: 0.7269 (t) REVERT: K 568 ASP cc_start: 0.8233 (p0) cc_final: 0.7965 (p0) REVERT: K 586 ASN cc_start: 0.9135 (t0) cc_final: 0.8877 (t0) outliers start: 30 outliers final: 20 residues processed: 180 average time/residue: 0.7820 time to fit residues: 152.1470 Evaluate side-chains 184 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 51 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 101 optimal weight: 0.0050 chunk 25 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060635 restraints weight = 37191.265| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.27 r_work: 0.2798 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17175 Z= 0.135 Angle : 0.668 8.810 24462 Z= 0.367 Chirality : 0.045 0.314 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.574 178.846 4613 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.92 % Allowed : 17.81 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.63 (0.25), residues: 1259 helix: 1.68 (0.19), residues: 776 sheet: -2.13 (0.67), residues: 69 loop : -1.60 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.009 0.001 TYR C 57 PHE 0.009 0.001 PHE K 574 TRP 0.018 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (17175) covalent geometry : angle 0.66816 / 0.37 (24462) hydrogen bonds : bond 0.04265 / 2.74 ( 926) hydrogen bonds : angle 3.21141 / 2.28 ( 2378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8841 (pm20) cc_final: 0.8386 (pm20) REVERT: B 24 ASP cc_start: 0.8369 (t0) cc_final: 0.8117 (t0) REVERT: C 90 ASP cc_start: 0.8294 (t0) cc_final: 0.8058 (t0) REVERT: D 68 GLU cc_start: 0.8349 (pt0) cc_final: 0.8145 (tp30) REVERT: E 59 GLU cc_start: 0.8490 (pm20) cc_final: 0.7876 (pm20) REVERT: E 77 ASP cc_start: 0.9013 (m-30) cc_final: 0.8738 (m-30) REVERT: F 85 ASP cc_start: 0.8804 (m-30) cc_final: 0.8525 (m-30) REVERT: G 64 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: G 73 ASN cc_start: 0.8367 (m-40) cc_final: 0.7769 (t0) REVERT: H 65 ASP cc_start: 0.8690 (t70) cc_final: 0.8169 (t0) REVERT: H 102 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8475 (tm-30) REVERT: K 196 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8674 (tt) REVERT: K 263 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: K 294 CYS cc_start: 0.8094 (m) cc_final: 0.7235 (t) REVERT: K 568 ASP cc_start: 0.8233 (p0) cc_final: 0.7961 (p0) REVERT: K 586 ASN cc_start: 0.9109 (t0) cc_final: 0.8891 (t0) outliers start: 32 outliers final: 18 residues processed: 181 average time/residue: 0.7281 time to fit residues: 142.5682 Evaluate side-chains 180 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.0060 chunk 145 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060057 restraints weight = 37211.199| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.28 r_work: 0.2781 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17175 Z= 0.175 Angle : 0.674 9.364 24462 Z= 0.368 Chirality : 0.046 0.331 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.512 179.240 4613 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.65 % Allowed : 18.45 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.64 (0.25), residues: 1259 helix: 1.69 (0.19), residues: 776 sheet: -2.16 (0.66), residues: 69 loop : -1.59 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.010 0.001 TYR H 34 PHE 0.011 0.001 PHE K 385 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (17175) covalent geometry : angle 0.67373 / 0.37 (24462) hydrogen bonds : bond 0.04528 / 2.89 ( 926) hydrogen bonds : angle 3.20294 / 2.28 ( 2378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8836 (pm20) cc_final: 0.8381 (pm20) REVERT: B 24 ASP cc_start: 0.8430 (t0) cc_final: 0.8189 (t0) REVERT: D 68 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: E 59 GLU cc_start: 0.8531 (pm20) cc_final: 0.7929 (pm20) REVERT: E 77 ASP cc_start: 0.9007 (m-30) cc_final: 0.8733 (m-30) REVERT: F 85 ASP cc_start: 0.8819 (m-30) cc_final: 0.8527 (m-30) REVERT: G 64 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: G 73 ASN cc_start: 0.8355 (m-40) cc_final: 0.7736 (t0) REVERT: H 65 ASP cc_start: 0.8692 (t70) cc_final: 0.8173 (t0) REVERT: H 102 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8430 (tm-30) REVERT: K 196 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8653 (tt) REVERT: K 263 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8902 (mp0) REVERT: K 294 CYS cc_start: 0.8138 (m) cc_final: 0.7283 (t) REVERT: K 385 PHE cc_start: 0.6394 (t80) cc_final: 0.5998 (t80) REVERT: K 568 ASP cc_start: 0.8236 (p0) cc_final: 0.7975 (p0) REVERT: K 586 ASN cc_start: 0.9125 (t0) cc_final: 0.8908 (t0) outliers start: 29 outliers final: 20 residues processed: 177 average time/residue: 0.7456 time to fit residues: 142.6665 Evaluate side-chains 184 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060110 restraints weight = 37188.907| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.26 r_work: 0.2781 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17175 Z= 0.180 Angle : 0.673 8.957 24462 Z= 0.367 Chirality : 0.046 0.328 2778 Planarity : 0.004 0.057 2087 Dihedral : 30.509 178.943 4613 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.37 % Allowed : 18.90 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.63 (0.25), residues: 1259 helix: 1.68 (0.19), residues: 775 sheet: -2.17 (0.66), residues: 69 loop : -1.59 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.010 0.001 TYR A 54 PHE 0.009 0.001 PHE K 385 TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS K 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (17175) covalent geometry : angle 0.67304 / 0.37 (24462) hydrogen bonds : bond 0.04431 / 2.83 ( 926) hydrogen bonds : angle 3.19822 / 2.27 ( 2378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8838 (pm20) cc_final: 0.8379 (pm20) REVERT: B 24 ASP cc_start: 0.8424 (t0) cc_final: 0.8185 (t0) REVERT: D 68 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: E 59 GLU cc_start: 0.8496 (pm20) cc_final: 0.7887 (pm20) REVERT: E 77 ASP cc_start: 0.9005 (m-30) cc_final: 0.8731 (m-30) REVERT: F 85 ASP cc_start: 0.8813 (m-30) cc_final: 0.8516 (m-30) REVERT: G 64 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: G 73 ASN cc_start: 0.8355 (m-40) cc_final: 0.7657 (t0) REVERT: G 75 LYS cc_start: 0.8580 (mttm) cc_final: 0.8328 (mmmt) REVERT: H 65 ASP cc_start: 0.8733 (t70) cc_final: 0.8208 (t0) REVERT: H 102 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8415 (tm-30) REVERT: K 196 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8640 (tt) REVERT: K 263 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8897 (mp0) REVERT: K 294 CYS cc_start: 0.8105 (m) cc_final: 0.7234 (t) REVERT: K 385 PHE cc_start: 0.6370 (t80) cc_final: 0.6006 (t80) REVERT: K 568 ASP cc_start: 0.8256 (p0) cc_final: 0.7998 (p0) REVERT: K 586 ASN cc_start: 0.9141 (t0) cc_final: 0.8903 (t0) outliers start: 26 outliers final: 19 residues processed: 174 average time/residue: 0.7332 time to fit residues: 137.7675 Evaluate side-chains 183 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 113 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.090195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.060291 restraints weight = 37316.519| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.29 r_work: 0.2787 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17175 Z= 0.153 Angle : 0.679 9.089 24462 Z= 0.369 Chirality : 0.046 0.322 2778 Planarity : 0.004 0.057 2087 Dihedral : 30.492 179.189 4613 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.74 % Allowed : 18.72 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.66 (0.25), residues: 1259 helix: 1.71 (0.19), residues: 775 sheet: -2.16 (0.66), residues: 69 loop : -1.58 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 95 TYR 0.011 0.001 TYR A 54 PHE 0.008 0.001 PHE B 61 TRP 0.016 0.001 TRP K 364 HIS 0.004 0.001 HIS K 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (17175) covalent geometry : angle 0.67912 / 0.37 (24462) hydrogen bonds : bond 0.04315 / 2.75 ( 926) hydrogen bonds : angle 3.18087 / 2.26 ( 2378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8833 (pm20) cc_final: 0.8373 (pm20) REVERT: B 24 ASP cc_start: 0.8416 (t0) cc_final: 0.8172 (t0) REVERT: C 90 ASP cc_start: 0.8296 (t0) cc_final: 0.8022 (t0) REVERT: D 68 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: E 59 GLU cc_start: 0.8502 (pm20) cc_final: 0.7893 (pm20) REVERT: E 77 ASP cc_start: 0.9005 (m-30) cc_final: 0.8727 (m-30) REVERT: F 85 ASP cc_start: 0.8812 (m-30) cc_final: 0.8511 (m-30) REVERT: G 64 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: G 73 ASN cc_start: 0.8342 (m-40) cc_final: 0.7630 (t0) REVERT: G 75 LYS cc_start: 0.8572 (mttm) cc_final: 0.8310 (mmmt) REVERT: H 65 ASP cc_start: 0.8690 (t70) cc_final: 0.8123 (t0) REVERT: H 102 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8416 (tm-30) REVERT: K 196 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8642 (tt) REVERT: K 263 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: K 294 CYS cc_start: 0.8104 (m) cc_final: 0.7284 (t) REVERT: K 299 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8527 (p) REVERT: K 385 PHE cc_start: 0.6326 (t80) cc_final: 0.5948 (t80) REVERT: K 568 ASP cc_start: 0.8263 (p0) cc_final: 0.8005 (p0) REVERT: K 586 ASN cc_start: 0.9139 (t0) cc_final: 0.8924 (t0) outliers start: 30 outliers final: 21 residues processed: 176 average time/residue: 0.7754 time to fit residues: 147.2216 Evaluate side-chains 185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 20 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.057968 restraints weight = 37119.429| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.32 r_work: 0.2767 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17175 Z= 0.252 Angle : 0.727 10.340 24462 Z= 0.389 Chirality : 0.048 0.347 2778 Planarity : 0.004 0.057 2087 Dihedral : 30.605 179.195 4613 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.47 % Allowed : 19.00 % Favored : 78.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.38 % 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: 0.49 (0.24), residues: 1259 helix: 1.58 (0.19), residues: 777 sheet: -2.22 (0.66), residues: 69 loop : -1.69 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.014 0.001 TYR A 54 PHE 0.012 0.001 PHE K 385 TRP 0.013 0.001 TRP K 364 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (17175) covalent geometry : angle 0.72683 / 0.39 (24462) hydrogen bonds : bond 0.05099 / 3.26 ( 926) hydrogen bonds : angle 3.30789 / 2.36 ( 2378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.42 seconds wall clock time: 89 minutes 8.37 seconds (5348.37 seconds total)