Starting phenix.real_space_refine on Sat Sep 12 01:18:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wv1_66279/09_2026/9wv1_66279.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wv1_66279/09_2026/9wv1_66279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wv1_66279/09_2026/9wv1_66279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wv1_66279/09_2026/9wv1_66279.map" model { file = "/net/cci-nas-00/data/ceres_data/9wv1_66279/09_2026/9wv1_66279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wv1_66279/09_2026/9wv1_66279.cif" } resolution = 3.1 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= 0.005 sd= 0.072 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 P 2 5.49 5 S 127 5.16 5 C 7992 2.51 5 N 2187 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12667 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1077 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 1 Chain: "B" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2767 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 20, 'TRANS': 334} Chain breaks: 1 Chain: "C" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1700 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 9, 'TRANS': 203} Chain: "D" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 572 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "E" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 511 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "F" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 536 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "G" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 532 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "H" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 532 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "I" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 482 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "J" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 697 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "K" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "L" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 638 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "M" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "N" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 606 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'R16': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'3PE': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'3PE:plan-2': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.27, per 1000 atoms: 0.18 Number of scatterers: 12667 At special positions: 0 Unit cell: (115.9, 117.8, 172.9, 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) S 127 16.00 P 2 15.00 O 2359 8.00 N 2187 7.00 C 7992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 32 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 52 " distance=2.03 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 48 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 52 " distance=2.03 Simple disulfide: pdb=" SG CYS F 32 " - pdb=" SG CYS F 48 " distance=2.03 Simple disulfide: pdb=" SG CYS G 29 " - pdb=" SG CYS G 54 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 54 " distance=2.03 Simple disulfide: pdb=" SG CYS H 33 " - pdb=" SG CYS H 50 " distance=2.03 Simple disulfide: pdb=" SG CYS I 29 " - pdb=" SG CYS I 54 " distance=2.03 Simple disulfide: pdb=" SG CYS I 33 " - pdb=" SG CYS I 50 " distance=2.03 Simple disulfide: pdb=" SG CYS J 28 " - pdb=" SG CYS J 52 " distance=2.04 Simple disulfide: pdb=" SG CYS J 32 " - pdb=" SG CYS J 48 " distance=2.03 Simple disulfide: pdb=" SG CYS K 28 " - pdb=" SG CYS K 52 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 48 " distance=2.03 Simple disulfide: pdb=" SG CYS L 28 " - pdb=" SG CYS L 52 " distance=2.04 Simple disulfide: pdb=" SG CYS L 32 " - pdb=" SG CYS L 48 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 54 " distance=2.03 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 50 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 54 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 50 " distance=2.03 Simple disulfide: pdb=" SG CYS O 29 " - pdb=" SG CYS O 54 " distance=2.03 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 50 " distance=2.03 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: 0.79 Conformation dependent library (CDL) restraints added in 452.3 milliseconds 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2978 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 5 sheets defined 71.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.928A pdb=" N LEU A 47 " --> pdb=" O PRO A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.576A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 148 Processing helix chain 'A' and resid 151 through 168 removed outlier: 4.274A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 Processing helix chain 'B' and resid 23 through 51 removed outlier: 3.780A pdb=" N TRP B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.308A pdb=" N LYS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.838A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.767A pdb=" N TRP B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.604A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 removed outlier: 4.165A pdb=" N GLU B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 56 Processing helix chain 'C' and resid 56 through 76 removed outlier: 3.714A pdb=" N ALA C 60 " --> pdb=" O ARG C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 95 Processing helix chain 'C' and resid 96 through 97 No H-bonds generated for 'chain 'C' and resid 96 through 97' Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.942A pdb=" N ARG C 102 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 120 Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.522A pdb=" N PHE C 159 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.681A pdb=" N LEU C 190 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS C 191 " --> pdb=" O GLU C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.653A pdb=" N ARG C 197 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 198' Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 215 through 218 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.649A pdb=" N GLU C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 33 removed outlier: 3.674A pdb=" N VAL D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 79 removed outlier: 3.551A pdb=" N ASN D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU D 76 " --> pdb=" O ILE D 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 28 Processing helix chain 'E' and resid 42 through 71 removed outlier: 3.524A pdb=" N LEU E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR E 60 " --> pdb=" O TYR E 56 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG E 62 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 33 removed outlier: 3.602A pdb=" N PHE F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS F 32 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL F 33 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 67 removed outlier: 3.514A pdb=" N GLU F 50 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F 62 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER F 64 " --> pdb=" O THR F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 removed outlier: 3.739A pdb=" N ILE F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 33 Processing helix chain 'G' and resid 44 through 75 removed outlier: 3.884A pdb=" N ASP G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 34 Processing helix chain 'H' and resid 44 through 75 removed outlier: 3.942A pdb=" N SER H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 23 removed outlier: 3.941A pdb=" N MET I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA I 19 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 31 removed outlier: 4.499A pdb=" N SER I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 72 removed outlier: 3.578A pdb=" N GLU I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG I 64 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 33 removed outlier: 4.067A pdb=" N LEU J 11 " --> pdb=" O GLN J 7 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG J 12 " --> pdb=" O GLN J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 85 removed outlier: 3.780A pdb=" N GLN J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) Proline residue: J 72 - end of helix Processing helix chain 'K' and resid 7 through 33 Processing helix chain 'K' and resid 42 through 80 removed outlier: 3.717A pdb=" N GLN K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU K 69 " --> pdb=" O MET K 65 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR K 70 " --> pdb=" O ARG K 66 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS K 71 " --> pdb=" O PHE K 67 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU K 78 " --> pdb=" O GLN K 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA K 79 " --> pdb=" O ASN K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 33 Processing helix chain 'L' and resid 42 through 82 removed outlier: 3.660A pdb=" N CYS L 48 " --> pdb=" O GLU L 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 34 removed outlier: 4.490A pdb=" N GLU M 12 " --> pdb=" O GLN M 8 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU M 13 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL M 15 " --> pdb=" O ALA M 11 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLU M 16 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP M 20 " --> pdb=" O GLU M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 85 removed outlier: 3.599A pdb=" N ASP M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN M 85 " --> pdb=" O LYS M 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 34 removed outlier: 3.581A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 77 removed outlier: 3.602A pdb=" N VAL N 49 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS N 50 " --> pdb=" O GLY N 46 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP N 60 " --> pdb=" O SER N 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP N 76 " --> pdb=" O LEU N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 34 removed outlier: 3.679A pdb=" N CYS O 33 " --> pdb=" O CYS O 29 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL O 34 " --> pdb=" O HIS O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 72 removed outlier: 3.603A pdb=" N GLY O 66 " --> pdb=" O HIS O 62 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS O 67 " --> pdb=" O GLU O 63 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 94 through 99 removed outlier: 6.498A pdb=" N ALA B 63 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL B 98 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 65 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS B 62 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE B 120 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR B 64 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ALA B 122 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N PHE B 66 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 119 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE B 152 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 121 " --> pdb=" O ILE B 152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.324A pdb=" N VAL B 188 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 404 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU B 190 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 402 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA4, first strand: chain 'B' and resid 258 through 259 removed outlier: 3.668A pdb=" N THR B 258 " --> pdb=" O ASP B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 127 removed outlier: 3.961A pdb=" N CYS C 130 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER C 131 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 166 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 133 " --> pdb=" O LEU C 164 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2514 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: 1.86 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2534 1.33 - 1.45: 2896 1.45 - 1.58: 7266 1.58 - 1.70: 5 1.70 - 1.83: 188 Bond restraints: 12889 Sorted by residual: bond pdb=" CB PRO A 51 " pdb=" CG PRO A 51 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.29e+00 bond pdb=" CG ARG I 24 " pdb=" CD ARG I 24 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CA ASP N 2 " pdb=" C ASP N 2 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.10e-02 2.27e+03 1.09e+00 bond pdb=" CB MET H 18 " pdb=" CG MET H 18 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.71e-01 bond pdb=" CA ASP B 386 " pdb=" CB ASP B 386 " ideal model delta sigma weight residual 1.530 1.546 -0.015 1.69e-02 3.50e+03 8.30e-01 ... (remaining 12884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 17062 1.98 - 3.97: 182 3.97 - 5.95: 34 5.95 - 7.94: 10 7.94 - 9.92: 3 Bond angle restraints: 17291 Sorted by residual: angle pdb=" N LYS G 39 " pdb=" CA LYS G 39 " pdb=" C LYS G 39 " ideal model delta sigma weight residual 114.56 108.15 6.41 1.27e+00 6.20e-01 2.55e+01 angle pdb=" CA PRO A 51 " pdb=" N PRO A 51 " pdb=" CD PRO A 51 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.36e+01 angle pdb=" CB MET E 65 " pdb=" CG MET E 65 " pdb=" SD MET E 65 " ideal model delta sigma weight residual 112.70 122.28 -9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C ALA B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" CA MET E 65 " pdb=" CB MET E 65 " pdb=" CG MET E 65 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.87e+00 ... (remaining 17286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 6590 18.10 - 36.21: 1016 36.21 - 54.31: 349 54.31 - 72.41: 69 72.41 - 90.52: 22 Dihedral angle restraints: 8046 sinusoidal: 3459 harmonic: 4587 Sorted by residual: dihedral pdb=" CB CYS F 28 " pdb=" SG CYS F 28 " pdb=" SG CYS F 52 " pdb=" CB CYS F 52 " ideal model delta sinusoidal sigma weight residual -86.00 -170.86 84.86 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS H 33 " pdb=" SG CYS H 33 " pdb=" SG CYS H 50 " pdb=" CB CYS H 50 " ideal model delta sinusoidal sigma weight residual -86.00 -156.82 70.82 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS E 32 " pdb=" SG CYS E 32 " pdb=" SG CYS E 48 " pdb=" CB CYS E 48 " ideal model delta sinusoidal sigma weight residual 93.00 51.96 41.04 1 1.00e+01 1.00e-02 2.36e+01 ... (remaining 8043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1358 0.036 - 0.073: 399 0.073 - 0.109: 99 0.109 - 0.145: 21 0.145 - 0.182: 4 Chirality restraints: 1881 Sorted by residual: chirality pdb=" CA ASP B 386 " pdb=" N ASP B 386 " pdb=" C ASP B 386 " pdb=" CB ASP B 386 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA THR B 143 " pdb=" N THR B 143 " pdb=" C THR B 143 " pdb=" CB THR B 143 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA MET H 17 " pdb=" N MET H 17 " pdb=" C MET H 17 " pdb=" CB MET H 17 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.09e-01 ... (remaining 1878 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 38 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO A 39 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 85 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO B 86 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 200 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO C 201 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " -0.031 5.00e-02 4.00e+02 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1887 2.76 - 3.29: 11599 3.29 - 3.83: 20596 3.83 - 4.36: 22106 4.36 - 4.90: 40479 Nonbonded interactions: 96667 Sorted by model distance: nonbonded pdb=" NZ LYS B 352 " pdb=" O LEU B 358 " model vdw 2.220 3.120 nonbonded pdb=" OG SER B 158 " pdb=" OG SER B 161 " model vdw 2.221 3.040 nonbonded pdb=" O LEU B 110 " pdb=" NH1 ARG B 138 " model vdw 2.259 3.120 nonbonded pdb=" OH TYR A 25 " pdb=" OE1 GLN K 13 " model vdw 2.267 3.040 nonbonded pdb=" OG SER O 44 " pdb=" OE1 GLU O 47 " model vdw 2.271 3.040 ... (remaining 96662 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 12 through 71) selection = chain 'E' selection = (chain 'F' and resid 12 through 71) selection = (chain 'K' and resid 12 through 71) selection = (chain 'L' and resid 12 through 71) } ncs_group { reference = (chain 'G' and resid 13 through 72) selection = (chain 'H' and resid 13 through 72) selection = chain 'I' selection = (chain 'N' and resid 13 through 72) selection = (chain 'O' and resid 13 through 72) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.230 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.003 0.091 12914 Z= 0.134 Angle : 0.554 9.920 17341 Z= 0.284 Chirality : 0.038 0.182 1881 Planarity : 0.005 0.084 2210 Dihedral : 19.692 90.518 4993 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.22 % Allowed : 32.75 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.22), residues: 1537 helix: 2.01 (0.16), residues: 1035 sheet: 0.53 (0.50), residues: 118 loop : -1.44 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 24 TYR 0.012 0.001 TYR K 21 PHE 0.011 0.001 PHE D 29 TRP 0.010 0.001 TRP B 28 HIS 0.005 0.001 HIS M 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (12889) covalent geometry : angle 0.55006 / 0.28 (17291) SS BOND : bond 0.00258 / 0.16 ( 25) SS BOND : angle 1.30220 / 0.84 ( 50) hydrogen bonds : bond 0.15598 / 10.45 ( 856) hydrogen bonds : angle 5.07010 / 3.69 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 MET cc_start: 0.5178 (mmp) cc_final: 0.4841 (mmp) outliers start: 3 outliers final: 1 residues processed: 194 average time/residue: 0.1184 time to fit residues: 32.2805 Evaluate side-chains 193 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 51 HIS E 68 GLN M 75 GLN O 23 ASN O 30 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164956 restraints weight = 15458.211| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.49 r_work: 0.3381 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12914 Z= 0.124 Angle : 0.512 6.967 17341 Z= 0.267 Chirality : 0.038 0.177 1881 Planarity : 0.004 0.066 2210 Dihedral : 6.224 62.819 1822 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.49 % Allowed : 30.34 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.22), residues: 1537 helix: 2.42 (0.16), residues: 1040 sheet: 0.64 (0.51), residues: 118 loop : -1.39 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 64 TYR 0.010 0.001 TYR K 21 PHE 0.008 0.001 PHE A 90 TRP 0.010 0.001 TRP B 28 HIS 0.004 0.001 HIS M 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12889) covalent geometry : angle 0.50999 / 0.27 (17291) SS BOND : bond 0.00254 / 0.17 ( 25) SS BOND : angle 1.02661 / 0.67 ( 50) hydrogen bonds : bond 0.05468 / 3.67 ( 856) hydrogen bonds : angle 3.73799 / 2.70 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 231 LYS cc_start: 0.7258 (mttm) cc_final: 0.7026 (mttp) REVERT: E 14 PHE cc_start: 0.5581 (OUTLIER) cc_final: 0.4055 (p90) REVERT: I 25 MET cc_start: 0.6419 (mmp) cc_final: 0.5600 (mpp) REVERT: L 58 LYS cc_start: 0.8916 (mttm) cc_final: 0.8606 (mtpt) REVERT: M 5 ARG cc_start: 0.8306 (tpt90) cc_final: 0.7946 (tpt90) REVERT: M 42 GLU cc_start: 0.8846 (tp30) cc_final: 0.8640 (mm-30) REVERT: O 67 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8113 (mttm) outliers start: 34 outliers final: 13 residues processed: 213 average time/residue: 0.1203 time to fit residues: 36.1727 Evaluate side-chains 197 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain N residue 75 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 139 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 84 optimal weight: 0.0170 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 17 optimal weight: 0.0000 overall best weight: 0.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.201830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161798 restraints weight = 15670.975| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.49 r_work: 0.3368 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12914 Z= 0.102 Angle : 0.479 7.993 17341 Z= 0.245 Chirality : 0.037 0.196 1881 Planarity : 0.004 0.060 2210 Dihedral : 5.915 59.605 1822 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.34 % Allowed : 30.34 % Favored : 67.32 % 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: 2.48 (0.22), residues: 1537 helix: 2.75 (0.16), residues: 1036 sheet: 0.70 (0.52), residues: 118 loop : -1.33 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 53 TYR 0.007 0.001 TYR F 21 PHE 0.009 0.001 PHE B 383 TRP 0.010 0.001 TRP B 28 HIS 0.003 0.001 HIS H 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (12889) covalent geometry : angle 0.47764 / 0.24 (17291) SS BOND : bond 0.00215 / 0.14 ( 25) SS BOND : angle 0.91301 / 0.57 ( 50) hydrogen bonds : bond 0.04337 / 2.91 ( 856) hydrogen bonds : angle 3.48845 / 2.51 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 45 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7676 (mm-30) REVERT: E 14 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.4070 (p90) REVERT: G 42 GLU cc_start: 0.7977 (tp30) cc_final: 0.7755 (tp30) REVERT: I 25 MET cc_start: 0.5611 (mmp) cc_final: 0.4930 (mpp) REVERT: M 5 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7864 (tpt90) outliers start: 32 outliers final: 17 residues processed: 218 average time/residue: 0.1197 time to fit residues: 36.5615 Evaluate side-chains 202 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 75 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 59 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 GLN D 75 ASN M 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.160820 restraints weight = 15554.288| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.55 r_work: 0.3517 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12914 Z= 0.196 Angle : 0.570 8.255 17341 Z= 0.290 Chirality : 0.040 0.184 1881 Planarity : 0.004 0.072 2210 Dihedral : 6.270 58.960 1822 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.70 % Allowed : 30.04 % Favored : 67.25 % 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: 2.16 (0.22), residues: 1537 helix: 2.51 (0.16), residues: 1042 sheet: 0.56 (0.51), residues: 118 loop : -1.52 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 24 TYR 0.021 0.001 TYR K 21 PHE 0.015 0.001 PHE K 67 TRP 0.010 0.001 TRP C 115 HIS 0.006 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (12889) covalent geometry : angle 0.56591 / 0.29 (17291) SS BOND : bond 0.00383 / 0.23 ( 25) SS BOND : angle 1.40409 / 1.03 ( 50) hydrogen bonds : bond 0.05736 / 3.82 ( 856) hydrogen bonds : angle 3.57619 / 2.58 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 154 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (pp) REVERT: E 14 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.4101 (p90) REVERT: G 42 GLU cc_start: 0.7800 (tp30) cc_final: 0.7600 (tp30) REVERT: I 25 MET cc_start: 0.4902 (mmp) cc_final: 0.4504 (mpp) REVERT: M 5 ARG cc_start: 0.7947 (tpt90) cc_final: 0.7619 (tpt90) outliers start: 37 outliers final: 21 residues processed: 218 average time/residue: 0.1119 time to fit residues: 34.5349 Evaluate side-chains 211 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 75 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 ASN M 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.199047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161052 restraints weight = 15535.846| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.49 r_work: 0.3341 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12914 Z= 0.128 Angle : 0.515 8.307 17341 Z= 0.263 Chirality : 0.038 0.179 1881 Planarity : 0.004 0.067 2210 Dihedral : 6.132 59.060 1822 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.00 % Allowed : 30.77 % Favored : 66.23 % 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: 2.30 (0.22), residues: 1537 helix: 2.62 (0.16), residues: 1040 sheet: 0.63 (0.52), residues: 118 loop : -1.47 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.013 0.001 TYR K 21 PHE 0.010 0.001 PHE K 67 TRP 0.009 0.001 TRP B 28 HIS 0.005 0.001 HIS M 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (12889) covalent geometry : angle 0.51152 / 0.26 (17291) SS BOND : bond 0.00295 / 0.18 ( 25) SS BOND : angle 1.17674 / 0.82 ( 50) hydrogen bonds : bond 0.04953 / 3.30 ( 856) hydrogen bonds : angle 3.48272 / 2.51 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 PHE cc_start: 0.5654 (OUTLIER) cc_final: 0.4141 (p90) REVERT: F 47 THR cc_start: 0.8054 (p) cc_final: 0.7831 (t) REVERT: H 65 MET cc_start: 0.8134 (mmp) cc_final: 0.7875 (mmp) REVERT: I 25 MET cc_start: 0.6542 (mmp) cc_final: 0.5478 (mpp) REVERT: M 5 ARG cc_start: 0.8322 (tpt90) cc_final: 0.7930 (tpt90) outliers start: 41 outliers final: 23 residues processed: 217 average time/residue: 0.1248 time to fit residues: 37.7622 Evaluate side-chains 210 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain N residue 75 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 20 optimal weight: 0.0570 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.200755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160356 restraints weight = 15522.007| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.49 r_work: 0.3359 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12914 Z= 0.108 Angle : 0.489 8.350 17341 Z= 0.249 Chirality : 0.037 0.165 1881 Planarity : 0.004 0.064 2210 Dihedral : 5.938 58.694 1822 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.92 % Allowed : 30.48 % Favored : 66.59 % 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: 2.49 (0.22), residues: 1537 helix: 2.76 (0.16), residues: 1042 sheet: 0.67 (0.52), residues: 118 loop : -1.39 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.008 0.001 TYR K 21 PHE 0.008 0.001 PHE A 90 TRP 0.010 0.001 TRP B 28 HIS 0.004 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (12889) covalent geometry : angle 0.48602 / 0.25 (17291) SS BOND : bond 0.00261 / 0.17 ( 25) SS BOND : angle 1.10876 / 0.72 ( 50) hydrogen bonds : bond 0.04288 / 2.86 ( 856) hydrogen bonds : angle 3.36327 / 2.42 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.4144 (p90) REVERT: I 25 MET cc_start: 0.6747 (mmp) cc_final: 0.5704 (mpp) REVERT: M 5 ARG cc_start: 0.8300 (tpt90) cc_final: 0.7928 (tpt90) outliers start: 40 outliers final: 27 residues processed: 217 average time/residue: 0.1181 time to fit residues: 35.7963 Evaluate side-chains 215 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 76 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 30 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 10 GLN M 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.199497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162461 restraints weight = 15451.003| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.44 r_work: 0.3382 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12914 Z= 0.126 Angle : 0.512 9.149 17341 Z= 0.259 Chirality : 0.038 0.181 1881 Planarity : 0.004 0.066 2210 Dihedral : 5.991 59.067 1822 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.14 % Allowed : 30.26 % Favored : 66.59 % 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: 2.45 (0.22), residues: 1537 helix: 2.74 (0.16), residues: 1042 sheet: 0.60 (0.52), residues: 118 loop : -1.41 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 24 TYR 0.013 0.001 TYR K 21 PHE 0.009 0.001 PHE K 67 TRP 0.009 0.001 TRP B 28 HIS 0.004 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12889) covalent geometry : angle 0.50837 / 0.26 (17291) SS BOND : bond 0.00281 / 0.18 ( 25) SS BOND : angle 1.17945 / 0.75 ( 50) hydrogen bonds : bond 0.04641 / 3.09 ( 856) hydrogen bonds : angle 3.37029 / 2.43 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 386 ASP cc_start: 0.8303 (p0) cc_final: 0.8091 (p0) REVERT: E 14 PHE cc_start: 0.5655 (OUTLIER) cc_final: 0.4147 (p90) REVERT: H 44 SER cc_start: 0.5212 (OUTLIER) cc_final: 0.4796 (t) REVERT: I 25 MET cc_start: 0.6591 (mmp) cc_final: 0.5530 (mpp) outliers start: 43 outliers final: 29 residues processed: 221 average time/residue: 0.1207 time to fit residues: 37.4601 Evaluate side-chains 218 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 76 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 ASN M 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.198484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.161171 restraints weight = 15250.284| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.42 r_work: 0.3377 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12914 Z= 0.152 Angle : 0.540 9.567 17341 Z= 0.274 Chirality : 0.039 0.183 1881 Planarity : 0.004 0.068 2210 Dihedral : 6.113 59.127 1822 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.92 % Allowed : 30.77 % Favored : 66.30 % 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: 2.34 (0.22), residues: 1537 helix: 2.66 (0.16), residues: 1042 sheet: 0.56 (0.52), residues: 118 loop : -1.48 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 24 TYR 0.016 0.001 TYR K 21 PHE 0.012 0.001 PHE K 67 TRP 0.009 0.001 TRP C 115 HIS 0.005 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12889) covalent geometry : angle 0.53620 / 0.27 (17291) SS BOND : bond 0.00316 / 0.20 ( 25) SS BOND : angle 1.27285 / 0.81 ( 50) hydrogen bonds : bond 0.05055 / 3.37 ( 856) hydrogen bonds : angle 3.42620 / 2.46 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 PHE cc_start: 0.5719 (OUTLIER) cc_final: 0.4093 (p90) REVERT: H 44 SER cc_start: 0.4107 (OUTLIER) cc_final: 0.3639 (t) REVERT: I 25 MET cc_start: 0.5397 (mmp) cc_final: 0.4907 (mpp) REVERT: M 5 ARG cc_start: 0.8108 (tpt170) cc_final: 0.7876 (tpt90) outliers start: 40 outliers final: 32 residues processed: 217 average time/residue: 0.1194 time to fit residues: 35.8931 Evaluate side-chains 223 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain N residue 21 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 ASN M 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.197671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.161880 restraints weight = 15395.847| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.49 r_work: 0.3525 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12914 Z= 0.173 Angle : 0.567 10.037 17341 Z= 0.287 Chirality : 0.040 0.186 1881 Planarity : 0.004 0.070 2210 Dihedral : 6.248 58.438 1822 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.85 % Allowed : 30.85 % Favored : 66.30 % 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: 2.25 (0.22), residues: 1537 helix: 2.61 (0.16), residues: 1036 sheet: 0.54 (0.52), residues: 118 loop : -1.52 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.019 0.001 TYR K 21 PHE 0.014 0.001 PHE K 67 TRP 0.009 0.001 TRP C 115 HIS 0.005 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (12889) covalent geometry : angle 0.56257 / 0.29 (17291) SS BOND : bond 0.00341 / 0.22 ( 25) SS BOND : angle 1.36476 / 0.87 ( 50) hydrogen bonds : bond 0.05380 / 3.58 ( 856) hydrogen bonds : angle 3.48433 / 2.51 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 PHE cc_start: 0.5547 (OUTLIER) cc_final: 0.4034 (p90) REVERT: H 44 SER cc_start: 0.3187 (OUTLIER) cc_final: 0.2811 (t) REVERT: M 5 ARG cc_start: 0.7869 (tpt170) cc_final: 0.7669 (tpt90) outliers start: 39 outliers final: 31 residues processed: 219 average time/residue: 0.1156 time to fit residues: 35.4457 Evaluate side-chains 221 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.0070 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 ASN M 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.198457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163846 restraints weight = 15528.231| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.43 r_work: 0.3527 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12914 Z= 0.146 Angle : 0.555 10.209 17341 Z= 0.280 Chirality : 0.039 0.183 1881 Planarity : 0.004 0.071 2210 Dihedral : 6.170 58.063 1822 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.63 % Allowed : 30.70 % Favored : 66.67 % 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: 2.28 (0.22), residues: 1537 helix: 2.62 (0.16), residues: 1038 sheet: 0.56 (0.52), residues: 118 loop : -1.47 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 24 TYR 0.015 0.001 TYR K 21 PHE 0.011 0.001 PHE K 67 TRP 0.009 0.001 TRP B 28 HIS 0.004 0.001 HIS O 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (12889) covalent geometry : angle 0.55085 / 0.28 (17291) SS BOND : bond 0.00302 / 0.19 ( 25) SS BOND : angle 1.32663 / 0.84 ( 50) hydrogen bonds : bond 0.05062 / 3.38 ( 856) hydrogen bonds : angle 3.45659 / 2.49 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3074 Ramachandran restraints generated. 1537 Oldfield, 0 Emsley, 1537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 14 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.4075 (p90) REVERT: H 44 SER cc_start: 0.3257 (OUTLIER) cc_final: 0.2868 (t) REVERT: I 25 MET cc_start: 0.4637 (mmp) cc_final: 0.4273 (mpp) outliers start: 36 outliers final: 31 residues processed: 216 average time/residue: 0.1220 time to fit residues: 36.4480 Evaluate side-chains 218 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 125 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 18 MET Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 64 ARG Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 4 GLN Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 12 GLU Chi-restraints excluded: chain N residue 21 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 75 ASN M 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.199275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163923 restraints weight = 15406.903| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.47 r_work: 0.3410 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12914 Z= 0.120 Angle : 0.527 10.006 17341 Z= 0.267 Chirality : 0.038 0.194 1881 Planarity : 0.004 0.067 2210 Dihedral : 5.921 58.649 1822 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.41 % Allowed : 30.99 % Favored : 66.59 % 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: 2.42 (0.22), residues: 1537 helix: 2.71 (0.16), residues: 1044 sheet: 0.59 (0.52), residues: 118 loop : -1.45 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.016 0.001 TYR I 58 PHE 0.008 0.001 PHE A 90 TRP 0.011 0.001 TRP B 28 HIS 0.004 0.001 HIS M 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (12889) covalent geometry : angle 0.52401 / 0.27 (17291) SS BOND : bond 0.00267 / 0.17 ( 25) SS BOND : angle 1.23829 / 0.76 ( 50) hydrogen bonds : bond 0.04516 / 3.01 ( 856) hydrogen bonds : angle 3.37920 / 2.43 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3520.95 seconds wall clock time: 60 minutes 46.60 seconds (3646.60 seconds total)