Starting phenix.real_space_refine on Sun May 3 18:38:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11yz_76206/05_2026/11yz_76206.cif Found real_map, /net/cci-nas-00/data/ceres_data/11yz_76206/05_2026/11yz_76206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11yz_76206/05_2026/11yz_76206.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11yz_76206/05_2026/11yz_76206.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11yz_76206/05_2026/11yz_76206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11yz_76206/05_2026/11yz_76206.map" } resolution = 2.77 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= 0.003 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: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 80 5.16 5 C 9160 2.51 5 N 2620 2.21 5 O 2740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14610 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "B" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "C" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "E" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "F" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "G" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "H" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "I" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "J" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1460 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 624 SG CYS A 90 44.039 100.556 47.259 1.00122.31 S ATOM 1190 SG CYS A 163 46.648 100.248 44.854 1.00118.19 S ATOM 2084 SG CYS B 90 29.002 54.681 26.547 1.00114.94 S ATOM 2650 SG CYS B 163 31.299 53.231 29.013 1.00119.76 S ATOM 3544 SG CYS C 90 91.637 99.989 47.228 1.00119.27 S ATOM 4110 SG CYS C 163 92.212 97.441 44.672 1.00120.67 S ATOM 5004 SG CYS D 90 43.316 99.996 26.513 1.00108.72 S ATOM 5570 SG CYS D 163 42.763 97.422 29.084 1.00106.13 S ATOM 6464 SG CYS E 90 105.839 54.459 47.274 1.00120.35 S ATOM 7030 SG CYS E 163 103.610 53.154 44.729 1.00120.68 S ATOM 7924 SG CYS F 90 90.948 100.497 26.443 1.00107.79 S ATOM 8490 SG CYS F 163 88.289 100.017 28.930 1.00105.43 S ATOM 9384 SG CYS G 90 67.023 26.918 47.331 1.00119.19 S ATOM 9950 SG CYS G 163 65.082 28.694 44.640 1.00121.14 S ATOM 10844 SG CYS H 90 106.069 55.256 26.524 1.00 99.86 S ATOM 11410 SG CYS H 163 105.080 57.781 29.088 1.00 99.22 S ATOM 12304 SG CYS I 90 28.757 55.377 47.313 1.00107.34 S ATOM 12870 SG CYS I 163 29.895 57.715 44.783 1.00107.33 S ATOM 13764 SG CYS J 90 67.888 26.924 26.469 1.00102.20 S ATOM 14330 SG CYS J 163 69.694 28.855 28.997 1.00102.79 S Time building chain proxies: 3.25, per 1000 atoms: 0.22 Number of scatterers: 14610 At special positions: 0 Unit cell: (134.9, 130.64, 74.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 80 16.00 O 2740 8.00 N 2620 7.00 C 9160 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: 1.00 Conformation dependent library (CDL) restraints added in 540.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 93 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 163 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 90 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 93 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 163 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 90 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 93 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 163 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 93 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 163 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 90 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 93 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 163 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 90 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 93 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 163 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 93 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 163 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 90 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 93 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 163 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 90 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 93 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 163 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 90 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 93 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 163 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 90 " 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3520 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 13 sheets defined 52.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.622A pdb=" N GLY A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 removed outlier: 4.053A pdb=" N VAL A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 57 through 60 Processing helix chain 'A' and resid 62 through 66 removed outlier: 3.791A pdb=" N VAL A 66 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 132 through 149 Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.665A pdb=" N THR B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'C' and resid 17 through 33 removed outlier: 3.563A pdb=" N GLY C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 42 removed outlier: 3.783A pdb=" N VAL C 42 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 Processing helix chain 'C' and resid 57 through 60 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.524A pdb=" N SER C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'D' and resid 17 through 33 Processing helix chain 'D' and resid 38 through 42 removed outlier: 3.712A pdb=" N VAL D 42 " --> pdb=" O ASP D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 Processing helix chain 'D' and resid 57 through 60 Processing helix chain 'D' and resid 62 through 67 removed outlier: 3.614A pdb=" N LEU D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 132 through 149 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 188 through 200 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.568A pdb=" N GLY E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 removed outlier: 3.781A pdb=" N VAL E 42 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 56 Processing helix chain 'E' and resid 57 through 60 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.520A pdb=" N SER E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 66 " --> pdb=" O PRO E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 66' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 132 through 149 Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.854A pdb=" N ARG E 167 " --> pdb=" O CYS E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 188 through 200 Processing helix chain 'F' and resid 17 through 33 Processing helix chain 'F' and resid 38 through 42 removed outlier: 3.714A pdb=" N VAL F 42 " --> pdb=" O ASP F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 56 Processing helix chain 'F' and resid 57 through 61 removed outlier: 3.883A pdb=" N THR F 61 " --> pdb=" O GLY F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 66 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 132 through 149 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 188 through 200 Processing helix chain 'G' and resid 17 through 33 removed outlier: 3.564A pdb=" N GLY G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.833A pdb=" N VAL G 42 " --> pdb=" O ASP G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 56 Processing helix chain 'G' and resid 57 through 60 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.508A pdb=" N LEU G 67 " --> pdb=" O ASP G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'G' and resid 164 through 168 Processing helix chain 'G' and resid 184 through 188 Processing helix chain 'G' and resid 188 through 200 Processing helix chain 'H' and resid 17 through 33 Processing helix chain 'H' and resid 38 through 42 removed outlier: 3.757A pdb=" N VAL H 42 " --> pdb=" O ASP H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 56 Processing helix chain 'H' and resid 57 through 60 Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.608A pdb=" N LEU H 67 " --> pdb=" O ASP H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 128 Processing helix chain 'H' and resid 132 through 149 Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 184 through 188 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'I' and resid 17 through 33 removed outlier: 3.503A pdb=" N ALA I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 42 removed outlier: 3.804A pdb=" N VAL I 42 " --> pdb=" O ASP I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 56 Processing helix chain 'I' and resid 57 through 60 Processing helix chain 'I' and resid 62 through 67 removed outlier: 3.534A pdb=" N LEU I 67 " --> pdb=" O ASP I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 132 through 149 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'J' and resid 17 through 33 Processing helix chain 'J' and resid 38 through 42 removed outlier: 3.668A pdb=" N VAL J 42 " --> pdb=" O ASP J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 56 Processing helix chain 'J' and resid 57 through 60 Processing helix chain 'J' and resid 62 through 66 Processing helix chain 'J' and resid 115 through 128 Processing helix chain 'J' and resid 132 through 149 Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 188 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 131 removed outlier: 8.412A pdb=" N GLN A 131 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR A 89 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 83 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA A 101 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY A 99 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR A 87 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE A 97 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 152 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 71 removed outlier: 3.508A pdb=" N MET B 70 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 130 through 131 removed outlier: 8.835A pdb=" N GLN B 131 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N THR B 89 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 83 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA B 101 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY B 99 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR B 87 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 97 " --> pdb=" O TYR B 87 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY B 152 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 131 removed outlier: 8.498A pdb=" N GLN C 131 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR C 89 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 83 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA C 101 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY C 99 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR C 87 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE C 97 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY C 152 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 130 through 131 removed outlier: 8.789A pdb=" N GLN D 131 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR D 89 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU D 80 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR D 105 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS D 82 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 103 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY D 152 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 130 through 131 removed outlier: 8.391A pdb=" N GLN E 131 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR E 89 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU E 83 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA E 101 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY E 99 " --> pdb=" O PRO E 85 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TYR E 87 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE E 97 " --> pdb=" O TYR E 87 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY E 152 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 131 removed outlier: 8.492A pdb=" N GLN F 131 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR F 89 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU F 83 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA F 101 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY F 99 " --> pdb=" O PRO F 85 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR F 87 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE F 97 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY F 152 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 130 through 131 removed outlier: 8.426A pdb=" N GLN G 131 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR G 89 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 83 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA G 101 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY G 99 " --> pdb=" O PRO G 85 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR G 87 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE G 97 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY G 152 " --> pdb=" O ILE G 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 131 removed outlier: 8.708A pdb=" N GLN H 131 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR H 89 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 83 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ALA H 101 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY H 99 " --> pdb=" O PRO H 85 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR H 87 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE H 97 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS H 98 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY H 152 " --> pdb=" O ILE H 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 130 through 131 removed outlier: 8.369A pdb=" N GLN I 131 " --> pdb=" O TYR I 87 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR I 89 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU I 83 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA I 101 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY I 99 " --> pdb=" O PRO I 85 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR I 87 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE I 97 " --> pdb=" O TYR I 87 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY I 152 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 70 through 71 Processing sheet with id=AB4, first strand: chain 'J' and resid 130 through 131 removed outlier: 8.401A pdb=" N GLN J 131 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR J 89 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU J 83 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA J 101 " --> pdb=" O GLU J 83 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY J 99 " --> pdb=" O PRO J 85 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N TYR J 87 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE J 97 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY J 152 " --> pdb=" O ILE J 106 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2289 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5030 1.34 - 1.46: 3002 1.46 - 1.58: 6668 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14840 Sorted by residual: bond pdb=" CB GLN J 19 " pdb=" CG GLN J 19 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CB GLN F 19 " pdb=" CG GLN F 19 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CB GLN D 19 " pdb=" CG GLN D 19 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CB GLN B 19 " pdb=" CG GLN B 19 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CA ASP J 149 " pdb=" C ASP J 149 " ideal model delta sigma weight residual 1.532 1.525 0.007 6.50e-03 2.37e+04 1.31e+00 ... (remaining 14835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 18799 0.78 - 1.56: 1071 1.56 - 2.34: 103 2.34 - 3.12: 49 3.12 - 3.90: 68 Bond angle restraints: 20090 Sorted by residual: angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 113.42 109.81 3.61 1.17e+00 7.31e-01 9.49e+00 angle pdb=" CA GLY A 104 " pdb=" C GLY A 104 " pdb=" N TYR A 105 " ideal model delta sigma weight residual 115.49 117.87 -2.38 1.03e+00 9.43e-01 5.35e+00 angle pdb=" CA GLY C 104 " pdb=" C GLY C 104 " pdb=" N TYR C 105 " ideal model delta sigma weight residual 115.49 117.80 -2.31 1.03e+00 9.43e-01 5.02e+00 angle pdb=" CA VAL B 169 " pdb=" C VAL B 169 " pdb=" N ARG B 170 " ideal model delta sigma weight residual 118.90 117.05 1.85 9.40e-01 1.13e+00 3.86e+00 angle pdb=" CA VAL B 169 " pdb=" C VAL B 169 " pdb=" O VAL B 169 " ideal model delta sigma weight residual 118.90 120.53 -1.63 8.80e-01 1.29e+00 3.45e+00 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 8507 17.26 - 34.52: 453 34.52 - 51.78: 111 51.78 - 69.04: 25 69.04 - 86.30: 4 Dihedral angle restraints: 9100 sinusoidal: 3650 harmonic: 5450 Sorted by residual: dihedral pdb=" CA GLN D 131 " pdb=" C GLN D 131 " pdb=" N VAL D 132 " pdb=" CA VAL D 132 " ideal model delta harmonic sigma weight residual 180.00 163.82 16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA GLN B 131 " pdb=" C GLN B 131 " pdb=" N VAL B 132 " pdb=" CA VAL B 132 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA ASP F 39 " pdb=" CB ASP F 39 " pdb=" CG ASP F 39 " pdb=" OD1 ASP F 39 " ideal model delta sinusoidal sigma weight residual -30.00 -84.82 54.82 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 9097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1592 0.028 - 0.057: 425 0.057 - 0.085: 123 0.085 - 0.113: 121 0.113 - 0.141: 69 Chirality restraints: 2330 Sorted by residual: chirality pdb=" CA ILE J 84 " pdb=" N ILE J 84 " pdb=" C ILE J 84 " pdb=" CB ILE J 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE C 84 " pdb=" N ILE C 84 " pdb=" C ILE C 84 " pdb=" CB ILE C 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ILE E 84 " pdb=" N ILE E 84 " pdb=" C ILE E 84 " pdb=" CB ILE E 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2327 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 35 " -0.016 5.00e-02 4.00e+02 2.45e-02 9.61e-01 pdb=" N PRO D 36 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 35 " 0.015 5.00e-02 4.00e+02 2.20e-02 7.77e-01 pdb=" N PRO G 36 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO G 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO G 36 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 35 " 0.014 5.00e-02 4.00e+02 2.19e-02 7.64e-01 pdb=" N PRO J 36 " -0.038 5.00e-02 4.00e+02 pdb=" CA PRO J 36 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO J 36 " 0.012 5.00e-02 4.00e+02 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 21 2.57 - 3.15: 12352 3.15 - 3.73: 21669 3.73 - 4.32: 30243 4.32 - 4.90: 53014 Nonbonded interactions: 117299 Sorted by model distance: nonbonded pdb=" OD2 ASP F 74 " pdb="ZN ZN H 301 " model vdw 1.986 2.230 nonbonded pdb=" OD2 ASP I 74 " pdb="ZN ZN G 301 " model vdw 1.987 2.230 nonbonded pdb=" OD2 ASP H 74 " pdb="ZN ZN J 301 " model vdw 1.988 2.230 nonbonded pdb=" OD2 ASP B 74 " pdb="ZN ZN D 301 " model vdw 1.988 2.230 nonbonded pdb=" OD2 ASP J 74 " pdb="ZN ZN B 301 " model vdw 1.988 2.230 ... (remaining 117294 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 4.060 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: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.390 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 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 : 0.007 0.275 14870 Z= 0.259 Angle : 0.455 3.898 20090 Z= 0.246 Chirality : 0.041 0.141 2330 Planarity : 0.003 0.025 2620 Dihedral : 11.581 86.296 5580 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 0.38 % Allowed : 6.67 % Favored : 92.95 % 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: 2.58 (0.20), residues: 1860 helix: 3.39 (0.19), residues: 750 sheet: 1.92 (0.24), residues: 430 loop : -0.47 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 50 TYR 0.008 0.001 TYR A 105 PHE 0.010 0.001 PHE E 97 HIS 0.001 0.000 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00227 (14840) covalent geometry : angle 0.45541 (20090) hydrogen bonds : bond 0.12949 ( 827) hydrogen bonds : angle 5.41477 ( 2289) metal coordination : bond 0.15741 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 278 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7726 (p0) REVERT: B 160 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8336 (mp0) REVERT: D 188 ASN cc_start: 0.8533 (t0) cc_final: 0.8265 (t0) REVERT: E 160 GLU cc_start: 0.7877 (mp0) cc_final: 0.7658 (mp0) REVERT: F 131 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8337 (mt0) REVERT: G 146 LYS cc_start: 0.9439 (ttpp) cc_final: 0.9172 (ttpp) REVERT: G 188 ASN cc_start: 0.8742 (t0) cc_final: 0.8514 (t0) REVERT: H 160 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8448 (mp0) REVERT: I 188 ASN cc_start: 0.8733 (t0) cc_final: 0.8436 (t0) outliers start: 6 outliers final: 1 residues processed: 284 average time/residue: 0.6052 time to fit residues: 189.0221 Evaluate side-chains 209 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain J residue 39 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.0030 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN D 131 GLN E 18 GLN J 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052717 restraints weight = 35365.404| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.53 r_work: 0.2678 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14870 Z= 0.134 Angle : 0.549 7.759 20090 Z= 0.281 Chirality : 0.043 0.143 2330 Planarity : 0.003 0.024 2620 Dihedral : 4.265 29.414 2094 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.40 % Favored : 98.49 % Rotamer: Outliers : 1.99 % Allowed : 13.72 % Favored : 84.29 % 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: 2.60 (0.20), residues: 1860 helix: 3.45 (0.19), residues: 750 sheet: 1.72 (0.24), residues: 450 loop : -0.42 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.007 0.001 TYR D 105 PHE 0.016 0.002 PHE J 16 HIS 0.001 0.000 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00307 (14840) covalent geometry : angle 0.54887 (20090) hydrogen bonds : bond 0.03691 ( 827) hydrogen bonds : angle 4.18236 ( 2289) metal coordination : bond 0.00430 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 0.656 Fit side-chains REVERT: A 17 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7535 (p0) REVERT: A 188 ASN cc_start: 0.8062 (t0) cc_final: 0.7805 (t0) REVERT: B 145 MET cc_start: 0.8584 (tpp) cc_final: 0.8335 (tpt) REVERT: B 160 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7788 (mp0) REVERT: B 188 ASN cc_start: 0.7824 (t0) cc_final: 0.7502 (t0) REVERT: C 67 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8368 (pp) REVERT: C 145 MET cc_start: 0.8503 (tpp) cc_final: 0.8180 (tpp) REVERT: C 188 ASN cc_start: 0.8040 (t0) cc_final: 0.7724 (t0) REVERT: D 39 ASP cc_start: 0.9157 (t0) cc_final: 0.8956 (p0) REVERT: D 188 ASN cc_start: 0.7799 (t0) cc_final: 0.7451 (t0) REVERT: E 146 LYS cc_start: 0.9393 (ttpp) cc_final: 0.9156 (ttpp) REVERT: E 160 GLU cc_start: 0.7810 (mp0) cc_final: 0.7480 (mp0) REVERT: E 188 ASN cc_start: 0.7977 (t0) cc_final: 0.7710 (t0) REVERT: F 131 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8328 (mt0) REVERT: F 174 SER cc_start: 0.8940 (m) cc_final: 0.8739 (m) REVERT: F 188 ASN cc_start: 0.7929 (t0) cc_final: 0.7636 (t0) REVERT: G 188 ASN cc_start: 0.8019 (t0) cc_final: 0.7727 (t0) REVERT: H 160 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8124 (mp0) REVERT: H 188 ASN cc_start: 0.7924 (t0) cc_final: 0.7645 (t0) REVERT: I 188 ASN cc_start: 0.7943 (t0) cc_final: 0.7592 (t0) REVERT: J 39 ASP cc_start: 0.9195 (t0) cc_final: 0.8993 (p0) REVERT: J 188 ASN cc_start: 0.8143 (t0) cc_final: 0.7900 (t0) outliers start: 31 outliers final: 4 residues processed: 240 average time/residue: 0.5593 time to fit residues: 148.7118 Evaluate side-chains 214 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 119 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 172 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 0.0670 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN E 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.052552 restraints weight = 36162.306| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.57 r_work: 0.2702 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14870 Z= 0.120 Angle : 0.515 6.495 20090 Z= 0.262 Chirality : 0.043 0.189 2330 Planarity : 0.003 0.027 2620 Dihedral : 4.194 29.374 2092 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.45 % Favored : 98.44 % Rotamer: Outliers : 1.86 % Allowed : 16.03 % Favored : 82.12 % 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: 2.61 (0.20), residues: 1860 helix: 3.41 (0.18), residues: 750 sheet: 2.05 (0.23), residues: 440 loop : -0.57 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 192 TYR 0.010 0.001 TYR D 87 PHE 0.015 0.001 PHE J 16 HIS 0.001 0.000 HIS G 102 Details of bonding type rmsd covalent geometry : bond 0.00280 (14840) covalent geometry : angle 0.51478 (20090) hydrogen bonds : bond 0.03363 ( 827) hydrogen bonds : angle 3.91229 ( 2289) metal coordination : bond 0.00462 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.587 Fit side-chains REVERT: A 17 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7796 (p0) REVERT: A 188 ASN cc_start: 0.8103 (t0) cc_final: 0.7765 (t0) REVERT: B 160 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7931 (mp0) REVERT: B 188 ASN cc_start: 0.7835 (t0) cc_final: 0.7495 (t0) REVERT: C 27 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: C 67 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8463 (pp) REVERT: C 188 ASN cc_start: 0.8112 (t0) cc_final: 0.7774 (t0) REVERT: D 39 ASP cc_start: 0.9179 (t0) cc_final: 0.8961 (p0) REVERT: D 188 ASN cc_start: 0.7841 (t0) cc_final: 0.7503 (t0) REVERT: E 27 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8563 (tm-30) REVERT: E 160 GLU cc_start: 0.8004 (mp0) cc_final: 0.7707 (mp0) REVERT: E 188 ASN cc_start: 0.8176 (t0) cc_final: 0.7838 (t0) REVERT: F 131 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8390 (mt0) REVERT: F 174 SER cc_start: 0.9050 (m) cc_final: 0.8846 (m) REVERT: F 188 ASN cc_start: 0.7907 (t0) cc_final: 0.7551 (t0) REVERT: G 188 ASN cc_start: 0.8088 (t0) cc_final: 0.7795 (t0) REVERT: H 160 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8246 (mp0) REVERT: H 188 ASN cc_start: 0.7999 (t0) cc_final: 0.7636 (t0) REVERT: I 188 ASN cc_start: 0.8010 (t0) cc_final: 0.7680 (t0) REVERT: J 188 ASN cc_start: 0.8146 (t0) cc_final: 0.7876 (t0) outliers start: 29 outliers final: 7 residues processed: 225 average time/residue: 0.5680 time to fit residues: 141.0023 Evaluate side-chains 212 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain I residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 45 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN E 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.052055 restraints weight = 37484.635| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.62 r_work: 0.2658 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14870 Z= 0.187 Angle : 0.548 6.966 20090 Z= 0.279 Chirality : 0.044 0.175 2330 Planarity : 0.003 0.023 2620 Dihedral : 4.322 30.298 2092 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.29 % Favored : 98.60 % Rotamer: Outliers : 3.21 % Allowed : 16.67 % Favored : 80.13 % 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: 2.44 (0.20), residues: 1860 helix: 3.29 (0.19), residues: 750 sheet: 1.75 (0.24), residues: 450 loop : -0.57 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 182 TYR 0.008 0.001 TYR E 60 PHE 0.012 0.001 PHE D 97 HIS 0.001 0.000 HIS C 102 Details of bonding type rmsd covalent geometry : bond 0.00439 (14840) covalent geometry : angle 0.54811 (20090) hydrogen bonds : bond 0.03622 ( 827) hydrogen bonds : angle 3.88239 ( 2289) metal coordination : bond 0.00752 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.606 Fit side-chains REVERT: A 17 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7812 (p0) REVERT: A 188 ASN cc_start: 0.8038 (t0) cc_final: 0.7710 (t0) REVERT: B 160 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7901 (mp0) REVERT: B 188 ASN cc_start: 0.7887 (t0) cc_final: 0.7538 (t0) REVERT: C 27 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: C 67 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8534 (pp) REVERT: C 188 ASN cc_start: 0.8138 (t0) cc_final: 0.7786 (t0) REVERT: D 188 ASN cc_start: 0.7908 (t0) cc_final: 0.7569 (t0) REVERT: E 27 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8320 (tm-30) REVERT: E 160 GLU cc_start: 0.8054 (mp0) cc_final: 0.7700 (mp0) REVERT: E 188 ASN cc_start: 0.8179 (t0) cc_final: 0.7829 (t0) REVERT: F 131 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8539 (mt0) REVERT: F 174 SER cc_start: 0.9075 (m) cc_final: 0.8874 (m) REVERT: F 188 ASN cc_start: 0.7990 (t0) cc_final: 0.7644 (t0) REVERT: G 188 ASN cc_start: 0.8022 (t0) cc_final: 0.7720 (t0) REVERT: H 146 LYS cc_start: 0.9299 (ttpp) cc_final: 0.9080 (ttpp) REVERT: H 160 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8190 (mp0) REVERT: H 188 ASN cc_start: 0.7991 (t0) cc_final: 0.7646 (t0) REVERT: I 188 ASN cc_start: 0.8002 (t0) cc_final: 0.7665 (t0) outliers start: 50 outliers final: 22 residues processed: 234 average time/residue: 0.5321 time to fit residues: 137.9440 Evaluate side-chains 217 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 51 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 139 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 116 optimal weight: 0.0670 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052201 restraints weight = 35759.415| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.55 r_work: 0.2693 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14870 Z= 0.106 Angle : 0.522 7.697 20090 Z= 0.265 Chirality : 0.042 0.173 2330 Planarity : 0.003 0.023 2620 Dihedral : 4.233 30.927 2092 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.34 % Favored : 98.55 % Rotamer: Outliers : 2.56 % Allowed : 18.65 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.20), residues: 1860 helix: 3.33 (0.19), residues: 750 sheet: 2.08 (0.23), residues: 440 loop : -0.72 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 167 TYR 0.009 0.001 TYR B 87 PHE 0.014 0.001 PHE J 16 HIS 0.004 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00246 (14840) covalent geometry : angle 0.52169 (20090) hydrogen bonds : bond 0.03142 ( 827) hydrogen bonds : angle 3.74713 ( 2289) metal coordination : bond 0.00280 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.607 Fit side-chains REVERT: A 17 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7785 (p0) REVERT: A 188 ASN cc_start: 0.7994 (t0) cc_final: 0.7656 (t0) REVERT: B 160 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7968 (mp0) REVERT: B 188 ASN cc_start: 0.7796 (t0) cc_final: 0.7435 (t0) REVERT: C 27 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: C 188 ASN cc_start: 0.8001 (t0) cc_final: 0.7643 (t0) REVERT: D 188 ASN cc_start: 0.7799 (t0) cc_final: 0.7450 (t0) REVERT: E 27 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: E 70 MET cc_start: 0.9248 (ptt) cc_final: 0.9043 (ptt) REVERT: E 160 GLU cc_start: 0.8050 (mp0) cc_final: 0.7707 (mp0) REVERT: E 188 ASN cc_start: 0.8147 (t0) cc_final: 0.7782 (t0) REVERT: F 61 THR cc_start: 0.8710 (t) cc_final: 0.8392 (p) REVERT: F 131 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8439 (mt0) REVERT: F 188 ASN cc_start: 0.7910 (t0) cc_final: 0.7549 (t0) REVERT: G 188 ASN cc_start: 0.8026 (t0) cc_final: 0.7721 (t0) REVERT: H 160 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8213 (mp0) REVERT: H 188 ASN cc_start: 0.8001 (t0) cc_final: 0.7643 (t0) REVERT: I 188 ASN cc_start: 0.7920 (t0) cc_final: 0.7585 (t0) outliers start: 40 outliers final: 10 residues processed: 228 average time/residue: 0.5530 time to fit residues: 139.2687 Evaluate side-chains 210 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 70 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.053646 restraints weight = 37581.117| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.61 r_work: 0.2697 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14870 Z= 0.116 Angle : 0.537 8.498 20090 Z= 0.269 Chirality : 0.043 0.167 2330 Planarity : 0.003 0.022 2620 Dihedral : 4.190 31.498 2092 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.24 % Favored : 98.66 % Rotamer: Outliers : 2.44 % Allowed : 19.23 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.20), residues: 1860 helix: 3.32 (0.19), residues: 750 sheet: 2.12 (0.23), residues: 440 loop : -0.67 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 182 TYR 0.008 0.001 TYR D 87 PHE 0.012 0.001 PHE J 16 HIS 0.003 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00273 (14840) covalent geometry : angle 0.53652 (20090) hydrogen bonds : bond 0.03114 ( 827) hydrogen bonds : angle 3.74188 ( 2289) metal coordination : bond 0.00361 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.610 Fit side-chains REVERT: A 17 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7789 (p0) REVERT: A 188 ASN cc_start: 0.7964 (t0) cc_final: 0.7608 (t0) REVERT: B 160 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7950 (mp0) REVERT: B 188 ASN cc_start: 0.7792 (t0) cc_final: 0.7426 (t0) REVERT: C 27 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: C 67 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8588 (pp) REVERT: C 188 ASN cc_start: 0.7985 (t0) cc_final: 0.7621 (t0) REVERT: D 145 MET cc_start: 0.8656 (tpp) cc_final: 0.8455 (tpt) REVERT: D 188 ASN cc_start: 0.7809 (t0) cc_final: 0.7457 (t0) REVERT: E 27 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: E 160 GLU cc_start: 0.8047 (mp0) cc_final: 0.7720 (mp0) REVERT: E 188 ASN cc_start: 0.8151 (t0) cc_final: 0.7780 (t0) REVERT: F 61 THR cc_start: 0.8685 (t) cc_final: 0.8364 (p) REVERT: F 131 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8438 (mt0) REVERT: F 188 ASN cc_start: 0.7903 (t0) cc_final: 0.7519 (t0) REVERT: G 188 ASN cc_start: 0.8029 (t0) cc_final: 0.7726 (t0) REVERT: H 160 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8216 (mp0) REVERT: H 188 ASN cc_start: 0.7965 (t0) cc_final: 0.7606 (t0) REVERT: I 188 ASN cc_start: 0.7922 (t0) cc_final: 0.7583 (t0) outliers start: 38 outliers final: 19 residues processed: 228 average time/residue: 0.5614 time to fit residues: 141.5544 Evaluate side-chains 219 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 55 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.052435 restraints weight = 34971.959| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.54 r_work: 0.2669 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14870 Z= 0.117 Angle : 0.538 9.267 20090 Z= 0.270 Chirality : 0.042 0.160 2330 Planarity : 0.002 0.023 2620 Dihedral : 4.173 31.835 2092 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.45 % Favored : 98.44 % Rotamer: Outliers : 2.82 % Allowed : 19.68 % Favored : 77.50 % 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: 2.53 (0.20), residues: 1860 helix: 3.34 (0.19), residues: 750 sheet: 2.13 (0.23), residues: 440 loop : -0.73 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 20 TYR 0.008 0.001 TYR H 87 PHE 0.010 0.001 PHE H 16 HIS 0.003 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00275 (14840) covalent geometry : angle 0.53808 (20090) hydrogen bonds : bond 0.03068 ( 827) hydrogen bonds : angle 3.70480 ( 2289) metal coordination : bond 0.00369 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.518 Fit side-chains REVERT: A 17 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7721 (p0) REVERT: A 188 ASN cc_start: 0.7828 (t0) cc_final: 0.7484 (t0) REVERT: B 145 MET cc_start: 0.8578 (ttm) cc_final: 0.8374 (tpp) REVERT: B 160 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7836 (mp0) REVERT: B 188 ASN cc_start: 0.7674 (t0) cc_final: 0.7318 (t0) REVERT: C 27 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8071 (tm-30) REVERT: C 188 ASN cc_start: 0.7857 (t0) cc_final: 0.7486 (t0) REVERT: D 188 ASN cc_start: 0.7674 (t0) cc_final: 0.7330 (t0) REVERT: E 27 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: E 39 ASP cc_start: 0.9382 (m-30) cc_final: 0.9151 (p0) REVERT: E 51 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8333 (p) REVERT: E 160 GLU cc_start: 0.7943 (mp0) cc_final: 0.7620 (mp0) REVERT: E 188 ASN cc_start: 0.8012 (t0) cc_final: 0.7646 (t0) REVERT: F 39 ASP cc_start: 0.9439 (m-30) cc_final: 0.9185 (p0) REVERT: F 131 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8380 (mt0) REVERT: F 188 ASN cc_start: 0.7775 (t0) cc_final: 0.7408 (t0) REVERT: G 188 ASN cc_start: 0.7930 (t0) cc_final: 0.7634 (t0) REVERT: H 160 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8140 (mp0) REVERT: H 188 ASN cc_start: 0.7842 (t0) cc_final: 0.7482 (t0) REVERT: I 27 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: I 188 ASN cc_start: 0.7797 (t0) cc_final: 0.7469 (t0) outliers start: 44 outliers final: 25 residues processed: 231 average time/residue: 0.5454 time to fit residues: 139.5248 Evaluate side-chains 225 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 55 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 169 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.050118 restraints weight = 34728.636| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.59 r_work: 0.2624 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14870 Z= 0.200 Angle : 0.594 11.360 20090 Z= 0.298 Chirality : 0.044 0.158 2330 Planarity : 0.003 0.023 2620 Dihedral : 4.343 31.722 2092 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.40 % Favored : 98.49 % Rotamer: Outliers : 2.95 % Allowed : 20.00 % Favored : 77.05 % 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: 2.36 (0.20), residues: 1860 helix: 3.29 (0.19), residues: 750 sheet: 1.77 (0.24), residues: 450 loop : -0.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 112 TYR 0.010 0.001 TYR H 87 PHE 0.014 0.001 PHE D 97 HIS 0.002 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00470 (14840) covalent geometry : angle 0.59439 (20090) hydrogen bonds : bond 0.03573 ( 827) hydrogen bonds : angle 3.77795 ( 2289) metal coordination : bond 0.00792 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.602 Fit side-chains REVERT: A 17 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7724 (p0) REVERT: A 188 ASN cc_start: 0.7875 (t0) cc_final: 0.7550 (t0) REVERT: B 160 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7844 (mp0) REVERT: B 167 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8769 (pmm-80) REVERT: B 188 ASN cc_start: 0.7775 (t0) cc_final: 0.7423 (t0) REVERT: C 27 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: C 67 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8611 (pp) REVERT: C 188 ASN cc_start: 0.7888 (t0) cc_final: 0.7521 (t0) REVERT: D 188 ASN cc_start: 0.7807 (t0) cc_final: 0.7472 (t0) REVERT: E 27 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: E 39 ASP cc_start: 0.9421 (m-30) cc_final: 0.9219 (p0) REVERT: E 145 MET cc_start: 0.8680 (tpp) cc_final: 0.8417 (tpp) REVERT: E 160 GLU cc_start: 0.7965 (mp0) cc_final: 0.7603 (mp0) REVERT: E 188 ASN cc_start: 0.8051 (t0) cc_final: 0.7689 (t0) REVERT: F 39 ASP cc_start: 0.9457 (m-30) cc_final: 0.9215 (p0) REVERT: F 131 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8525 (mt0) REVERT: F 188 ASN cc_start: 0.7854 (t0) cc_final: 0.7495 (t0) REVERT: G 188 ASN cc_start: 0.7878 (t0) cc_final: 0.7577 (t0) REVERT: H 160 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8102 (mp0) REVERT: H 188 ASN cc_start: 0.7904 (t0) cc_final: 0.7545 (t0) REVERT: I 27 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: I 188 ASN cc_start: 0.7838 (t0) cc_final: 0.7508 (t0) outliers start: 46 outliers final: 26 residues processed: 226 average time/residue: 0.5658 time to fit residues: 141.1502 Evaluate side-chains 224 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 51 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 122 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.051038 restraints weight = 34844.729| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.62 r_work: 0.2644 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14870 Z= 0.128 Angle : 0.567 9.779 20090 Z= 0.284 Chirality : 0.043 0.159 2330 Planarity : 0.002 0.023 2620 Dihedral : 4.272 32.325 2092 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.34 % Favored : 98.49 % Rotamer: Outliers : 2.50 % Allowed : 20.71 % Favored : 76.79 % 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: 2.40 (0.20), residues: 1860 helix: 3.30 (0.19), residues: 750 sheet: 2.03 (0.23), residues: 440 loop : -0.84 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 20 TYR 0.009 0.001 TYR B 87 PHE 0.012 0.001 PHE H 16 HIS 0.003 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00303 (14840) covalent geometry : angle 0.56656 (20090) hydrogen bonds : bond 0.03194 ( 827) hydrogen bonds : angle 3.68566 ( 2289) metal coordination : bond 0.00424 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.595 Fit side-chains REVERT: A 17 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7687 (p0) REVERT: A 39 ASP cc_start: 0.9437 (m-30) cc_final: 0.9217 (p0) REVERT: A 188 ASN cc_start: 0.7826 (t0) cc_final: 0.7498 (t0) REVERT: B 145 MET cc_start: 0.8592 (ttm) cc_final: 0.8315 (tpp) REVERT: B 160 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7871 (mp0) REVERT: B 188 ASN cc_start: 0.7731 (t0) cc_final: 0.7374 (t0) REVERT: C 27 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: C 188 ASN cc_start: 0.7832 (t0) cc_final: 0.7471 (t0) REVERT: D 188 ASN cc_start: 0.7756 (t0) cc_final: 0.7420 (t0) REVERT: E 27 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: E 160 GLU cc_start: 0.7942 (mp0) cc_final: 0.7593 (mp0) REVERT: E 188 ASN cc_start: 0.8016 (t0) cc_final: 0.7650 (t0) REVERT: F 39 ASP cc_start: 0.9474 (m-30) cc_final: 0.9221 (p0) REVERT: F 131 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8431 (mt0) REVERT: F 188 ASN cc_start: 0.7831 (t0) cc_final: 0.7481 (t0) REVERT: G 188 ASN cc_start: 0.7884 (t0) cc_final: 0.7584 (t0) REVERT: H 160 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8118 (mp0) REVERT: H 188 ASN cc_start: 0.7876 (t0) cc_final: 0.7515 (t0) REVERT: I 27 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8445 (tm-30) REVERT: I 145 MET cc_start: 0.8429 (ttm) cc_final: 0.8146 (tpt) REVERT: I 188 ASN cc_start: 0.7824 (t0) cc_final: 0.7487 (t0) outliers start: 39 outliers final: 24 residues processed: 223 average time/residue: 0.5792 time to fit residues: 142.1871 Evaluate side-chains 219 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 13 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 153 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.050984 restraints weight = 34594.040| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.60 r_work: 0.2643 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14870 Z= 0.144 Angle : 0.579 10.631 20090 Z= 0.290 Chirality : 0.043 0.155 2330 Planarity : 0.003 0.023 2620 Dihedral : 4.288 32.500 2092 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.61 % Favored : 98.23 % Rotamer: Outliers : 2.12 % Allowed : 21.35 % Favored : 76.54 % 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: 2.40 (0.20), residues: 1860 helix: 3.30 (0.19), residues: 750 sheet: 2.02 (0.23), residues: 440 loop : -0.86 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 182 TYR 0.011 0.001 TYR B 87 PHE 0.012 0.001 PHE H 16 HIS 0.006 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00340 (14840) covalent geometry : angle 0.57886 (20090) hydrogen bonds : bond 0.03250 ( 827) hydrogen bonds : angle 3.69622 ( 2289) metal coordination : bond 0.00500 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.671 Fit side-chains REVERT: A 17 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7690 (p0) REVERT: A 39 ASP cc_start: 0.9434 (m-30) cc_final: 0.9228 (p0) REVERT: A 188 ASN cc_start: 0.7852 (t0) cc_final: 0.7535 (t0) REVERT: B 160 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7861 (mp0) REVERT: B 188 ASN cc_start: 0.7745 (t0) cc_final: 0.7387 (t0) REVERT: C 27 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8065 (tm-30) REVERT: C 67 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8613 (pp) REVERT: C 188 ASN cc_start: 0.7830 (t0) cc_final: 0.7464 (t0) REVERT: D 188 ASN cc_start: 0.7773 (t0) cc_final: 0.7437 (t0) REVERT: E 27 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: E 51 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8341 (p) REVERT: E 145 MET cc_start: 0.8626 (tpp) cc_final: 0.8365 (tpp) REVERT: E 160 GLU cc_start: 0.7960 (mp0) cc_final: 0.7617 (mp0) REVERT: E 188 ASN cc_start: 0.8028 (t0) cc_final: 0.7661 (t0) REVERT: F 39 ASP cc_start: 0.9465 (m-30) cc_final: 0.9232 (p0) REVERT: F 131 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8434 (mt0) REVERT: F 188 ASN cc_start: 0.7825 (t0) cc_final: 0.7471 (t0) REVERT: G 188 ASN cc_start: 0.7867 (t0) cc_final: 0.7560 (t0) REVERT: H 160 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8109 (mp0) REVERT: H 188 ASN cc_start: 0.7868 (t0) cc_final: 0.7519 (t0) REVERT: I 27 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: I 145 MET cc_start: 0.8451 (ttm) cc_final: 0.8166 (tpt) REVERT: I 188 ASN cc_start: 0.7807 (t0) cc_final: 0.7476 (t0) outliers start: 33 outliers final: 24 residues processed: 217 average time/residue: 0.5493 time to fit residues: 131.6094 Evaluate side-chains 220 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain H residue 13 ILE Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 51 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 165 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.070067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.051778 restraints weight = 34543.610| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.60 r_work: 0.2664 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14870 Z= 0.113 Angle : 0.565 9.939 20090 Z= 0.282 Chirality : 0.042 0.157 2330 Planarity : 0.002 0.023 2620 Dihedral : 4.220 32.922 2092 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.18 % Favored : 98.60 % Rotamer: Outliers : 2.12 % Allowed : 21.54 % Favored : 76.35 % 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: 2.44 (0.20), residues: 1860 helix: 3.32 (0.19), residues: 750 sheet: 2.08 (0.23), residues: 440 loop : -0.85 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 167 TYR 0.009 0.001 TYR B 87 PHE 0.011 0.001 PHE H 16 HIS 0.004 0.000 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00266 (14840) covalent geometry : angle 0.56487 (20090) hydrogen bonds : bond 0.03040 ( 827) hydrogen bonds : angle 3.66994 ( 2289) metal coordination : bond 0.00303 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4173.46 seconds wall clock time: 72 minutes 4.75 seconds (4324.75 seconds total)