Starting phenix.real_space_refine on Sat Oct 24 05:53:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgp_9958/10_2026/7cgp_9958.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1 5.49 5 S 122 5.16 5 C 7823 2.51 5 N 2158 2.21 5 O 2329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12433 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1068 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain breaks: 1 Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2696 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 326} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1684 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 5, 'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 521 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 569 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 502 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "J" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 680 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 590 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 646 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "M" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 589 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "N" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 580 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "O" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.68, per 1000 atoms: 0.22 Number of scatterers: 12433 At special positions: 0 Unit cell: (121.68, 113.568, 172.38, 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 122 16.00 P 1 15.00 O 2329 8.00 N 2158 7.00 C 7823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 52 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS J 28 " - pdb=" SG CYS J 52 " distance=2.03 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS O 29 " - pdb=" SG CYS O 54 " distance=2.04 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: 1.04 Conformation dependent library (CDL) restraints added in 500.6 milliseconds 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 72.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 4.342A pdb=" N GLN A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 68 through 93 removed outlier: 3.878A pdb=" N LYS A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 148 Processing helix chain 'A' and resid 151 through 171 removed outlier: 3.990A pdb=" N SER A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 removed outlier: 3.572A pdb=" N ALA A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 51 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 124 through 137 removed outlier: 3.504A pdb=" N LEU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.883A pdb=" N HIS B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 183 " --> pdb=" O THR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 227 through 243 removed outlier: 3.940A pdb=" N ILE B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N HIS B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.720A pdb=" N ARG B 351 " --> pdb=" O THR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 Processing helix chain 'C' and resid 22 through 55 Processing helix chain 'C' and resid 58 through 75 Processing helix chain 'C' and resid 78 through 97 removed outlier: 4.557A pdb=" N GLU C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 119 removed outlier: 3.831A pdb=" N ARG C 119 " --> pdb=" O TRP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.514A pdb=" N ARG C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Proline residue: C 160 - end of helix removed outlier: 3.657A pdb=" N VAL C 163 " --> pdb=" O PRO C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.855A pdb=" N LEU C 190 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 4.294A 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 193 through 197 removed outlier: 3.620A pdb=" N LEU C 196 " --> pdb=" O PRO C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.516A pdb=" N ARG C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 244 Processing helix chain 'D' and resid 14 through 32 Processing helix chain 'D' and resid 42 through 76 removed outlier: 3.758A pdb=" N THR D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 30 removed outlier: 3.926A pdb=" N PHE E 17 " --> pdb=" O GLN E 13 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 75 Processing helix chain 'F' and resid 14 through 33 Processing helix chain 'F' and resid 42 through 75 removed outlier: 4.130A pdb=" N GLN F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 33 removed outlier: 3.621A pdb=" N MET G 21 " --> pdb=" O MET G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 75 removed outlier: 3.716A pdb=" N SER G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET G 74 " --> pdb=" O THR G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 34 Processing helix chain 'H' and resid 44 through 75 removed outlier: 4.004A pdb=" N ASP H 52 " --> pdb=" O SER H 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 34 removed outlier: 3.746A pdb=" N SER I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG I 31 " --> pdb=" O SER I 27 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS I 32 " --> pdb=" O ALA I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 49 removed outlier: 3.595A pdb=" N VAL I 49 " --> pdb=" O LYS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 73 removed outlier: 3.661A pdb=" N ARG I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 31 Processing helix chain 'J' and resid 42 through 85 Proline residue: J 72 - end of helix Processing helix chain 'K' and resid 9 through 32 Processing helix chain 'K' and resid 45 through 77 removed outlier: 3.812A pdb=" N SER K 49 " --> pdb=" O GLU K 45 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU K 50 " --> pdb=" O THR K 46 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA K 77 " --> pdb=" O GLN K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 33 removed outlier: 3.784A pdb=" N GLN L 10 " --> pdb=" O PRO L 6 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN L 13 " --> pdb=" O ASP L 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR L 27 " --> pdb=" O LYS L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 82 removed outlier: 4.397A pdb=" N SER L 49 " --> pdb=" O GLU L 45 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 34 Processing helix chain 'M' and resid 45 through 75 removed outlier: 4.673A pdb=" N LEU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE M 61 " --> pdb=" O LYS M 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 34 removed outlier: 3.593A pdb=" N CYS N 33 " --> pdb=" O CYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 removed outlier: 3.881A pdb=" N ASP N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 73 removed outlier: 3.752A pdb=" N GLY N 66 " --> pdb=" O HIS N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 34 removed outlier: 3.970A pdb=" N SER O 27 " --> pdb=" O ASN O 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG O 31 " --> pdb=" O SER O 27 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 77 removed outlier: 4.116A pdb=" N ASP O 52 " --> pdb=" O SER O 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS O 57 " --> pdb=" O ARG O 53 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU O 59 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP O 60 " --> pdb=" O SER O 56 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 77 " --> pdb=" O SER O 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.227A pdb=" N THR B 64 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA B 122 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE B 66 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 119 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE B 152 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 121 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 205 removed outlier: 6.213A pdb=" N VAL B 188 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU B 404 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU B 190 " --> pdb=" O ARG B 402 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 402 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 367 through 368 Processing sheet with id=AA4, first strand: chain 'C' and resid 125 through 126 876 hydrogen bonds defined for protein. 2592 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: 1.92 Time building geometry restraints manager: 1.30 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: 2477 1.33 - 1.45: 2878 1.45 - 1.58: 7115 1.58 - 1.70: 2 1.70 - 1.82: 179 Bond restraints: 12651 Sorted by residual: bond pdb=" N VAL C 22 " pdb=" CA VAL C 22 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N VAL C 27 " pdb=" CA VAL C 27 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.70e+00 bond pdb=" N LEU B 227 " pdb=" CA LEU B 227 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.19e-02 7.06e+03 7.53e+00 bond pdb=" N LYS C 24 " pdb=" CA LYS C 24 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.04e-02 9.25e+03 7.43e+00 bond pdb=" N THR B 157 " pdb=" CA THR B 157 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.08e+00 ... (remaining 12646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 16624 2.03 - 4.07: 364 4.07 - 6.10: 19 6.10 - 8.14: 0 8.14 - 10.17: 1 Bond angle restraints: 17008 Sorted by residual: angle pdb=" N VAL M 49 " pdb=" CA VAL M 49 " pdb=" C VAL M 49 " ideal model delta sigma weight residual 112.96 108.20 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" N LEU B 154 " pdb=" CA LEU B 154 " pdb=" C LEU B 154 " ideal model delta sigma weight residual 112.89 108.17 4.72 1.24e+00 6.50e-01 1.45e+01 angle pdb=" C ASP F 31 " pdb=" N CYS F 32 " pdb=" CA CYS F 32 " ideal model delta sigma weight residual 122.56 117.21 5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" N ARG C 197 " pdb=" CA ARG C 197 " pdb=" C ARG C 197 " ideal model delta sigma weight residual 113.50 109.23 4.27 1.23e+00 6.61e-01 1.21e+01 angle pdb=" O3P PEE C 301 " pdb=" P PEE C 301 " pdb=" O4P PEE C 301 " ideal model delta sigma weight residual 92.91 103.08 -10.17 3.00e+00 1.11e-01 1.15e+01 ... (remaining 17003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 7365 24.31 - 48.63: 423 48.63 - 72.94: 42 72.94 - 97.26: 13 97.26 - 121.57: 1 Dihedral angle restraints: 7844 sinusoidal: 3264 harmonic: 4580 Sorted by residual: dihedral pdb=" CB CYS F 32 " pdb=" SG CYS F 32 " pdb=" SG CYS F 48 " pdb=" CB CYS F 48 " ideal model delta sinusoidal sigma weight residual 93.00 52.07 40.93 1 1.00e+01 1.00e-02 2.35e+01 dihedral pdb=" CA CYS N 33 " pdb=" C CYS N 33 " pdb=" N VAL N 34 " pdb=" CA VAL N 34 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CB CYS D 32 " pdb=" SG CYS D 32 " pdb=" SG CYS D 48 " pdb=" CB CYS D 48 " ideal model delta sinusoidal sigma weight residual 93.00 56.44 36.56 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1558 0.051 - 0.102: 262 0.102 - 0.153: 43 0.153 - 0.204: 9 0.204 - 0.254: 1 Chirality restraints: 1873 Sorted by residual: chirality pdb=" CA VAL C 198 " pdb=" N VAL C 198 " pdb=" C VAL C 198 " pdb=" CB VAL C 198 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU B 154 " pdb=" N LEU B 154 " pdb=" C LEU B 154 " pdb=" CB LEU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA VAL C 27 " pdb=" N VAL C 27 " pdb=" C VAL C 27 " pdb=" CB VAL C 27 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 1870 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 196 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU C 196 " -0.071 2.00e-02 2.50e+03 pdb=" O LEU C 196 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG C 197 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 34 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO G 35 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO G 35 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 35 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 47 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C GLU N 47 " 0.026 2.00e-02 2.50e+03 pdb=" O GLU N 47 " -0.010 2.00e-02 2.50e+03 pdb=" N SER N 48 " -0.009 2.00e-02 2.50e+03 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 75 2.46 - 3.07: 9289 3.07 - 3.68: 18702 3.68 - 4.29: 25669 4.29 - 4.90: 42681 Nonbonded interactions: 96416 Sorted by model distance: nonbonded pdb=" OH TYR D 70 " pdb=" OE2 GLU G 63 " model vdw 1.852 3.040 nonbonded pdb=" O ILE B 335 " pdb=" OG1 THR B 363 " model vdw 1.882 3.040 nonbonded pdb=" NE2 GLN K 74 " pdb=" OE2 GLU O 63 " model vdw 1.951 3.120 nonbonded pdb=" OE2 GLU A 144 " pdb=" OG SER A 150 " model vdw 2.036 3.040 nonbonded pdb=" OH TYR F 21 " pdb=" O HIS G 62 " model vdw 2.068 3.040 ... (remaining 96411 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 13 through 72 or (resid 73 through 75 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 13 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 73 or (resid 74 through 75 and (na \ me N or name CA or name C or name O or name CB )))) selection = chain 'F' selection = (chain 'K' and (resid 13 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 72 or (resid 73 through 75 and (na \ me N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 73)) selection = (chain 'M' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'N' and (resid 10 through 13 or (resid 14 and (name N or name CA or name \ C or name O or name CB )) or resid 15 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 72 or (r \ esid 73 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 10 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 69 through 72 or (resid 73 and ( \ name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.380 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: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12677 Z= 0.306 Angle : 0.663 10.173 17060 Z= 0.425 Chirality : 0.041 0.254 1873 Planarity : 0.003 0.050 2183 Dihedral : 14.706 121.569 4790 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.53 % Allowed : 3.01 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.19), residues: 1531 helix: -0.96 (0.14), residues: 1038 sheet: -2.91 (0.44), residues: 105 loop : -3.36 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.023 0.002 TYR L 21 PHE 0.015 0.001 PHE B 80 TRP 0.013 0.001 TRP B 28 HIS 0.012 0.001 HIS O 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.31 (12651) covalent geometry : angle 0.65908 / 0.42 (17008) SS BOND : bond 0.00400 / 0.24 ( 26) SS BOND : angle 1.51254 / 0.90 ( 52) hydrogen bonds : bond 0.13426 / 8.94 ( 876) hydrogen bonds : angle 5.89083 / 4.33 ( 2592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 582 time to evaluate : 0.472 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7189 (ttp) cc_final: 0.6917 (mmt) REVERT: A 185 PHE cc_start: 0.8449 (t80) cc_final: 0.8159 (t80) REVERT: B 215 ARG cc_start: 0.7604 (tmt170) cc_final: 0.6615 (ttt-90) REVERT: B 219 VAL cc_start: 0.8842 (t) cc_final: 0.8623 (t) REVERT: B 329 ASP cc_start: 0.6102 (p0) cc_final: 0.5485 (p0) REVERT: C 76 LEU cc_start: 0.7117 (tp) cc_final: 0.6602 (pt) REVERT: C 206 SER cc_start: 0.9123 (p) cc_final: 0.8914 (p) REVERT: C 218 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8277 (tmtt) REVERT: D 57 LEU cc_start: 0.8841 (mt) cc_final: 0.7463 (mt) REVERT: E 18 LEU cc_start: 0.8662 (mt) cc_final: 0.8353 (pp) REVERT: E 22 ASN cc_start: 0.8532 (p0) cc_final: 0.8114 (p0) REVERT: E 51 HIS cc_start: 0.8472 (m170) cc_final: 0.7961 (m170) REVERT: E 58 LYS cc_start: 0.9363 (mtpt) cc_final: 0.8627 (mmmt) REVERT: E 60 THR cc_start: 0.9588 (m) cc_final: 0.9364 (p) REVERT: F 23 LYS cc_start: 0.8724 (mtmm) cc_final: 0.8465 (mttp) REVERT: F 62 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7341 (ttm-80) REVERT: G 20 ASP cc_start: 0.8188 (t70) cc_final: 0.7908 (t0) REVERT: H 40 GLU cc_start: 0.8528 (mp0) cc_final: 0.8273 (mp0) REVERT: H 49 VAL cc_start: 0.9229 (t) cc_final: 0.9003 (p) REVERT: H 57 LYS cc_start: 0.9419 (mttt) cc_final: 0.9122 (mtpt) REVERT: I 17 MET cc_start: 0.8927 (tpt) cc_final: 0.8683 (tmm) REVERT: I 21 MET cc_start: 0.8971 (tmm) cc_final: 0.8089 (tmm) REVERT: I 25 MET cc_start: 0.8851 (ptp) cc_final: 0.7498 (ptm) REVERT: I 44 SER cc_start: 0.7704 (m) cc_final: 0.7374 (p) REVERT: I 58 TYR cc_start: 0.8705 (t80) cc_final: 0.7844 (t80) REVERT: I 65 MET cc_start: 0.8711 (tpp) cc_final: 0.8291 (tpp) REVERT: I 69 LEU cc_start: 0.8593 (mm) cc_final: 0.7971 (mm) REVERT: M 14 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7985 (tm-30) REVERT: M 52 ASP cc_start: 0.7813 (m-30) cc_final: 0.7596 (m-30) REVERT: M 64 ARG cc_start: 0.7566 (mtt-85) cc_final: 0.7143 (mtt-85) REVERT: O 42 GLU cc_start: 0.7814 (tp30) cc_final: 0.7286 (tp30) outliers start: 7 outliers final: 5 residues processed: 586 average time/residue: 0.1320 time to fit residues: 104.6265 Evaluate side-chains 426 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 421 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain C residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 203 GLN E 54 GLN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS J 9 GLN K 71 HIS L 71 HIS L 74 GLN M 30 HIS N 8 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.123336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.097890 restraints weight = 28852.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097538 restraints weight = 18169.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098392 restraints weight = 18502.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.098710 restraints weight = 13066.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.098785 restraints weight = 12803.752| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 12677 Z= 0.171 Angle : 0.774 11.911 17060 Z= 0.396 Chirality : 0.044 0.287 1873 Planarity : 0.005 0.040 2183 Dihedral : 7.772 93.540 1734 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.08 % Allowed : 18.05 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1531 helix: 0.81 (0.16), residues: 1057 sheet: -2.17 (0.41), residues: 115 loop : -2.50 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 104 TYR 0.018 0.002 TYR C 124 PHE 0.023 0.002 PHE A 81 TRP 0.014 0.002 TRP B 225 HIS 0.011 0.001 HIS I 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (12651) covalent geometry : angle 0.75678 / 0.39 (17008) SS BOND : bond 0.00497 / 0.33 ( 26) SS BOND : angle 3.06865 / 1.83 ( 52) hydrogen bonds : bond 0.04971 / 3.30 ( 876) hydrogen bonds : angle 4.62300 / 3.43 ( 2592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 485 time to evaluate : 0.494 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8433 (pp20) cc_final: 0.7766 (tp30) REVERT: B 241 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8531 (mp) REVERT: B 329 ASP cc_start: 0.6440 (p0) cc_final: 0.5974 (p0) REVERT: B 390 TYR cc_start: 0.8036 (m-80) cc_final: 0.7804 (m-10) REVERT: C 76 LEU cc_start: 0.6690 (tp) cc_final: 0.6423 (pp) REVERT: C 134 TYR cc_start: 0.8807 (p90) cc_final: 0.8587 (p90) REVERT: C 143 SER cc_start: 0.9058 (t) cc_final: 0.8549 (t) REVERT: C 214 ASP cc_start: 0.7871 (m-30) cc_final: 0.7598 (m-30) REVERT: C 218 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8247 (tmtt) REVERT: D 57 LEU cc_start: 0.8589 (mt) cc_final: 0.7525 (mt) REVERT: F 20 THR cc_start: 0.9126 (p) cc_final: 0.8878 (t) REVERT: F 35 ASP cc_start: 0.8383 (p0) cc_final: 0.7999 (p0) REVERT: F 62 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.6418 (ttm-80) REVERT: F 66 ARG cc_start: 0.8696 (tpp-160) cc_final: 0.8382 (mpp-170) REVERT: G 13 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7878 (tp) REVERT: G 20 ASP cc_start: 0.8086 (t70) cc_final: 0.7786 (t0) REVERT: G 31 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8616 (ttm-80) REVERT: G 42 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7265 (mm-30) REVERT: H 25 MET cc_start: 0.8687 (ptm) cc_final: 0.8484 (ptm) REVERT: H 49 VAL cc_start: 0.8833 (t) cc_final: 0.8616 (p) REVERT: H 64 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8135 (ttm-80) REVERT: I 14 GLU cc_start: 0.8626 (tp30) cc_final: 0.8339 (tp30) REVERT: I 17 MET cc_start: 0.8511 (tpt) cc_final: 0.8283 (tmm) REVERT: I 21 MET cc_start: 0.8865 (tmm) cc_final: 0.8132 (tmm) REVERT: I 25 MET cc_start: 0.7934 (ptp) cc_final: 0.7326 (ptm) REVERT: I 58 TYR cc_start: 0.8123 (t80) cc_final: 0.7741 (t80) REVERT: I 60 ASP cc_start: 0.8483 (t0) cc_final: 0.8196 (t0) REVERT: I 64 ARG cc_start: 0.8196 (ptm-80) cc_final: 0.7844 (ptm-80) REVERT: J 9 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7704 (tp40) REVERT: J 77 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.8182 (ttp-110) REVERT: O 16 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6944 (mt-10) outliers start: 41 outliers final: 21 residues processed: 497 average time/residue: 0.1317 time to fit residues: 89.1982 Evaluate side-chains 434 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 411 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 28 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [98, 49, 97, 63, 26, 104, 13, 16, 81, 85, 78] chunk 98 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN E 51 HIS E 54 GLN F 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS J 13 ASN K 71 HIS L 73 GLN O 37 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096746 restraints weight = 29247.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096466 restraints weight = 19951.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097213 restraints weight = 20158.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098693 restraints weight = 14487.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.098575 restraints weight = 11680.223| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12677 Z= 0.168 Angle : 0.750 11.674 17060 Z= 0.386 Chirality : 0.043 0.217 1873 Planarity : 0.004 0.041 2183 Dihedral : 7.156 79.146 1730 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.59 % Allowed : 20.68 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1531 helix: 1.21 (0.16), residues: 1064 sheet: -1.60 (0.45), residues: 108 loop : -2.04 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 413 TYR 0.017 0.001 TYR L 70 PHE 0.017 0.001 PHE A 81 TRP 0.012 0.001 TRP B 244 HIS 0.010 0.001 HIS K 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (12651) covalent geometry : angle 0.73652 / 0.38 (17008) SS BOND : bond 0.00441 / 0.30 ( 26) SS BOND : angle 2.70231 / 1.63 ( 52) hydrogen bonds : bond 0.04809 / 3.22 ( 876) hydrogen bonds : angle 4.50082 / 3.34 ( 2592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 452 time to evaluate : 0.485 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8396 (pp20) cc_final: 0.7879 (tp30) REVERT: B 107 LYS cc_start: 0.8252 (mtmm) cc_final: 0.8029 (mttm) REVERT: B 113 MET cc_start: 0.8085 (ttm) cc_final: 0.7813 (ttm) REVERT: B 241 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8504 (mp) REVERT: B 390 TYR cc_start: 0.8141 (m-80) cc_final: 0.7937 (m-10) REVERT: C 134 TYR cc_start: 0.8878 (p90) cc_final: 0.8646 (p90) REVERT: C 143 SER cc_start: 0.9116 (t) cc_final: 0.8637 (t) REVERT: C 179 MET cc_start: 0.8312 (mmm) cc_final: 0.8069 (mmm) REVERT: C 218 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8300 (tmtt) REVERT: D 17 PHE cc_start: 0.8647 (t80) cc_final: 0.8326 (t80) REVERT: D 39 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8110 (tpt90) REVERT: D 53 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8374 (mm) REVERT: F 50 GLU cc_start: 0.7579 (pt0) cc_final: 0.7344 (tm-30) REVERT: F 62 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.6638 (ttm-80) REVERT: F 66 ARG cc_start: 0.8650 (tpp-160) cc_final: 0.8446 (mpp-170) REVERT: G 20 ASP cc_start: 0.8054 (t70) cc_final: 0.7795 (t0) REVERT: G 31 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8659 (ttm-80) REVERT: G 42 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7258 (mm-30) REVERT: H 31 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: I 21 MET cc_start: 0.8715 (tmm) cc_final: 0.7865 (tmm) REVERT: I 25 MET cc_start: 0.7877 (ptp) cc_final: 0.7631 (ptp) REVERT: I 58 TYR cc_start: 0.8084 (t80) cc_final: 0.7618 (t80) REVERT: J 9 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7929 (tp40) REVERT: J 13 ASN cc_start: 0.8178 (m110) cc_final: 0.7892 (m-40) REVERT: N 14 GLU cc_start: 0.5706 (mm-30) cc_final: 0.5484 (mm-30) REVERT: N 17 MET cc_start: 0.8382 (ttp) cc_final: 0.8105 (ttp) outliers start: 61 outliers final: 30 residues processed: 480 average time/residue: 0.1260 time to fit residues: 82.7133 Evaluate side-chains 431 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 399 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain L residue 28 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 73 GLN Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [143, 149, 31, 25, 13, 61, 10, 92, 26, 58, 103] chunk 143 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 0.0170 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS K 13 GLN N 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.121230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.096002 restraints weight = 29128.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095639 restraints weight = 20066.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096571 restraints weight = 20720.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.096961 restraints weight = 14411.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097241 restraints weight = 13285.859| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12677 Z= 0.161 Angle : 0.770 11.313 17060 Z= 0.389 Chirality : 0.044 0.329 1873 Planarity : 0.004 0.059 2183 Dihedral : 6.899 79.559 1729 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.59 % Allowed : 22.33 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.22), residues: 1531 helix: 1.37 (0.16), residues: 1059 sheet: -1.30 (0.46), residues: 110 loop : -1.97 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 64 TYR 0.020 0.002 TYR H 22 PHE 0.025 0.001 PHE A 81 TRP 0.013 0.001 TRP B 244 HIS 0.009 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12651) covalent geometry : angle 0.75484 / 0.38 (17008) SS BOND : bond 0.00428 / 0.29 ( 26) SS BOND : angle 2.82743 / 1.67 ( 52) hydrogen bonds : bond 0.04710 / 3.16 ( 876) hydrogen bonds : angle 4.41330 / 3.27 ( 2592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 447 time to evaluate : 0.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7601 (tp-100) REVERT: A 140 GLU cc_start: 0.8369 (pp20) cc_final: 0.7922 (tp30) REVERT: A 173 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7863 (mmmm) REVERT: B 241 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8459 (mp) REVERT: C 143 SER cc_start: 0.9135 (t) cc_final: 0.8687 (t) REVERT: C 218 LYS cc_start: 0.8590 (mtmm) cc_final: 0.8345 (tmtt) REVERT: D 17 PHE cc_start: 0.8755 (t80) cc_final: 0.8495 (t80) REVERT: E 27 THR cc_start: 0.9291 (p) cc_final: 0.9070 (t) REVERT: F 50 GLU cc_start: 0.7887 (pt0) cc_final: 0.7465 (tm-30) REVERT: F 62 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.6438 (ttm-80) REVERT: F 66 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8151 (mpp-170) REVERT: G 14 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7688 (mm-30) REVERT: G 20 ASP cc_start: 0.8083 (t70) cc_final: 0.7811 (t0) REVERT: G 31 ARG cc_start: 0.9101 (ttm-80) cc_final: 0.8789 (ttm-80) REVERT: G 42 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7374 (mm-30) REVERT: H 31 ARG cc_start: 0.8764 (mtm-85) cc_final: 0.8444 (mtm-85) REVERT: I 21 MET cc_start: 0.8735 (tmm) cc_final: 0.7804 (tmm) REVERT: I 25 MET cc_start: 0.8012 (ptp) cc_final: 0.7605 (ptp) REVERT: I 43 LEU cc_start: 0.8197 (tp) cc_final: 0.7979 (tp) REVERT: I 58 TYR cc_start: 0.8169 (t80) cc_final: 0.7627 (t80) REVERT: I 69 LEU cc_start: 0.8501 (mp) cc_final: 0.8287 (mp) REVERT: J 9 GLN cc_start: 0.8253 (tp-100) cc_final: 0.8015 (tp40) REVERT: K 31 ASP cc_start: 0.8755 (m-30) cc_final: 0.8478 (m-30) REVERT: K 40 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: L 76 GLU cc_start: 0.7783 (pp20) cc_final: 0.7529 (pp20) REVERT: M 14 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7593 (tm-30) REVERT: N 14 GLU cc_start: 0.5401 (mm-30) cc_final: 0.5006 (mm-30) REVERT: N 17 MET cc_start: 0.8378 (ttp) cc_final: 0.8161 (ttp) REVERT: N 20 ASP cc_start: 0.8001 (t0) cc_final: 0.7777 (t0) REVERT: O 12 GLU cc_start: 0.7983 (pp20) cc_final: 0.7442 (pp20) outliers start: 61 outliers final: 40 residues processed: 472 average time/residue: 0.1175 time to fit residues: 77.1478 Evaluate side-chains 451 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 409 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 52 CYS Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [116, 66, 64, 111, 39, 50, 61, 16, 27, 92, 119] chunk 116 optimal weight: 0.8980 chunk 66 optimal weight: 0.0010 chunk 64 optimal weight: 0.0670 chunk 111 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS F 71 HIS K 22 ASN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.121923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096429 restraints weight = 29112.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095306 restraints weight = 18924.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096542 restraints weight = 19719.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096882 restraints weight = 14403.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097049 restraints weight = 13712.994| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12677 Z= 0.147 Angle : 0.755 13.787 17060 Z= 0.378 Chirality : 0.044 0.355 1873 Planarity : 0.004 0.046 2183 Dihedral : 6.641 80.655 1729 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.49 % Allowed : 22.03 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1531 helix: 1.47 (0.16), residues: 1052 sheet: -1.04 (0.47), residues: 111 loop : -1.82 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 64 TYR 0.017 0.001 TYR M 38 PHE 0.022 0.001 PHE E 29 TRP 0.016 0.001 TRP B 244 HIS 0.009 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12651) covalent geometry : angle 0.74633 / 0.37 (17008) SS BOND : bond 0.00459 / 0.31 ( 26) SS BOND : angle 2.22473 / 1.29 ( 52) hydrogen bonds : bond 0.04545 / 3.06 ( 876) hydrogen bonds : angle 4.33281 / 3.20 ( 2592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 455 time to evaluate : 0.538 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7638 (tp-100) REVERT: B 113 MET cc_start: 0.8236 (ttm) cc_final: 0.8008 (ttm) REVERT: B 241 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8465 (mp) REVERT: C 134 TYR cc_start: 0.8866 (p90) cc_final: 0.8649 (p90) REVERT: C 143 SER cc_start: 0.9148 (t) cc_final: 0.8720 (t) REVERT: C 199 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8867 (t) REVERT: C 218 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8362 (tmtt) REVERT: D 17 PHE cc_start: 0.8746 (t80) cc_final: 0.8504 (t80) REVERT: D 23 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9121 (mttt) REVERT: D 39 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8165 (tpt90) REVERT: E 50 GLU cc_start: 0.8628 (tp30) cc_final: 0.8411 (tp30) REVERT: E 58 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8482 (pttt) REVERT: F 31 ASP cc_start: 0.8383 (m-30) cc_final: 0.8174 (m-30) REVERT: F 50 GLU cc_start: 0.7948 (pt0) cc_final: 0.7527 (tm-30) REVERT: F 66 ARG cc_start: 0.8776 (tpp-160) cc_final: 0.8381 (mpt-90) REVERT: G 20 ASP cc_start: 0.8044 (t70) cc_final: 0.7775 (t0) REVERT: G 31 ARG cc_start: 0.9060 (ttm-80) cc_final: 0.8734 (ttm-80) REVERT: H 31 ARG cc_start: 0.8728 (mtm-85) cc_final: 0.8436 (mtm-85) REVERT: I 21 MET cc_start: 0.8736 (tmm) cc_final: 0.7931 (tmm) REVERT: I 43 LEU cc_start: 0.8132 (tp) cc_final: 0.7909 (tp) REVERT: I 58 TYR cc_start: 0.8194 (t80) cc_final: 0.7831 (t80) REVERT: I 69 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8252 (tt) REVERT: J 8 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6623 (tm-30) REVERT: J 74 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8458 (tp) REVERT: K 40 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: L 76 GLU cc_start: 0.7779 (pp20) cc_final: 0.7552 (pp20) outliers start: 73 outliers final: 37 residues processed: 488 average time/residue: 0.1184 time to fit residues: 80.1176 Evaluate side-chains 446 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 404 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 52 CYS Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [49, 108, 25, 138, 38, 1, 84, 144, 22, 111, 115] chunk 49 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 25 optimal weight: 0.0870 chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS K 13 GLN M 62 HIS ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.120508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095102 restraints weight = 28879.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093698 restraints weight = 18943.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094549 restraints weight = 20087.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095858 restraints weight = 15155.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095854 restraints weight = 12930.449| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12677 Z= 0.163 Angle : 0.790 12.483 17060 Z= 0.401 Chirality : 0.045 0.313 1873 Planarity : 0.004 0.040 2183 Dihedral : 6.510 79.812 1728 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.66 % Allowed : 24.14 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.22), residues: 1531 helix: 1.47 (0.16), residues: 1057 sheet: -1.02 (0.53), residues: 88 loop : -1.85 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 64 TYR 0.021 0.001 TYR J 67 PHE 0.027 0.001 PHE E 29 TRP 0.017 0.001 TRP B 244 HIS 0.012 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (12651) covalent geometry : angle 0.77496 / 0.39 (17008) SS BOND : bond 0.00467 / 0.32 ( 26) SS BOND : angle 2.90541 / 1.73 ( 52) hydrogen bonds : bond 0.04667 / 3.13 ( 876) hydrogen bonds : angle 4.43179 / 3.27 ( 2592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 435 time to evaluate : 0.332 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7743 (tp-100) REVERT: B 107 LYS cc_start: 0.8204 (mttm) cc_final: 0.7779 (mttm) REVERT: B 241 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8449 (mp) REVERT: B 310 THR cc_start: 0.7997 (t) cc_final: 0.7513 (t) REVERT: C 143 SER cc_start: 0.9150 (t) cc_final: 0.8725 (t) REVERT: C 199 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8809 (t) REVERT: C 218 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8384 (tmtt) REVERT: D 23 LYS cc_start: 0.9387 (ttmt) cc_final: 0.9106 (mttt) REVERT: D 39 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8107 (tpt90) REVERT: D 45 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8400 (mp0) REVERT: E 50 GLU cc_start: 0.8575 (tp30) cc_final: 0.8300 (tp30) REVERT: E 58 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8433 (pttt) REVERT: E 62 ARG cc_start: 0.8224 (ttt90) cc_final: 0.8009 (ttt90) REVERT: F 50 GLU cc_start: 0.7914 (pt0) cc_final: 0.7297 (tm-30) REVERT: G 14 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7619 (mm-30) REVERT: G 20 ASP cc_start: 0.8008 (t70) cc_final: 0.7758 (t0) REVERT: G 22 TYR cc_start: 0.9047 (t80) cc_final: 0.8635 (t80) REVERT: G 31 ARG cc_start: 0.9062 (ttm-80) cc_final: 0.8762 (ttm-80) REVERT: H 31 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.7926 (mtm-85) REVERT: I 21 MET cc_start: 0.8813 (tmm) cc_final: 0.8595 (tmm) REVERT: I 43 LEU cc_start: 0.8117 (tp) cc_final: 0.7884 (tp) REVERT: J 13 ASN cc_start: 0.8004 (m110) cc_final: 0.7774 (m-40) REVERT: K 40 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: L 76 GLU cc_start: 0.7894 (pp20) cc_final: 0.7657 (pp20) outliers start: 62 outliers final: 44 residues processed: 464 average time/residue: 0.1151 time to fit residues: 74.0155 Evaluate side-chains 453 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 406 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [134, 148, 51, 59, 120, 147, 17, 46, 137, 74, 127] chunk 134 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN E 51 HIS F 71 HIS K 13 GLN L 54 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094385 restraints weight = 29120.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.092984 restraints weight = 21720.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093849 restraints weight = 22553.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095680 restraints weight = 16162.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095584 restraints weight = 12408.473| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12677 Z= 0.175 Angle : 0.801 12.667 17060 Z= 0.410 Chirality : 0.046 0.319 1873 Planarity : 0.004 0.040 2183 Dihedral : 6.378 79.238 1728 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.44 % Allowed : 25.94 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1531 helix: 1.46 (0.16), residues: 1052 sheet: -1.01 (0.52), residues: 93 loop : -1.70 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 64 TYR 0.021 0.002 TYR J 67 PHE 0.028 0.001 PHE A 81 TRP 0.017 0.001 TRP B 244 HIS 0.010 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (12651) covalent geometry : angle 0.78725 / 0.40 (17008) SS BOND : bond 0.00693 / 0.46 ( 26) SS BOND : angle 2.82451 / 1.69 ( 52) hydrogen bonds : bond 0.04713 / 3.15 ( 876) hydrogen bonds : angle 4.47811 / 3.29 ( 2592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 437 time to evaluate : 0.362 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7751 (tp-100) REVERT: A 72 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7668 (mttp) REVERT: A 140 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7892 (tp30) REVERT: A 154 ASN cc_start: 0.8191 (m110) cc_final: 0.7972 (m-40) REVERT: B 107 LYS cc_start: 0.8179 (mttm) cc_final: 0.7823 (mttm) REVERT: B 177 ASP cc_start: 0.7587 (t70) cc_final: 0.7372 (t70) REVERT: B 241 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 310 THR cc_start: 0.8105 (t) cc_final: 0.7781 (t) REVERT: C 179 MET cc_start: 0.8451 (mmm) cc_final: 0.8173 (mtp) REVERT: C 199 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8861 (t) REVERT: D 23 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9043 (mttm) REVERT: E 50 GLU cc_start: 0.8621 (tp30) cc_final: 0.8292 (tp30) REVERT: E 58 LYS cc_start: 0.8741 (mtmt) cc_final: 0.8455 (pttt) REVERT: E 62 ARG cc_start: 0.8263 (ttt90) cc_final: 0.7939 (ttt90) REVERT: F 50 GLU cc_start: 0.7879 (pt0) cc_final: 0.7344 (tm-30) REVERT: G 17 MET cc_start: 0.8327 (ppp) cc_final: 0.7637 (ppp) REVERT: G 20 ASP cc_start: 0.8075 (t70) cc_final: 0.7846 (t0) REVERT: G 31 ARG cc_start: 0.9076 (ttm-80) cc_final: 0.8792 (ttm-80) REVERT: I 21 MET cc_start: 0.8712 (tmm) cc_final: 0.8505 (tmm) REVERT: I 43 LEU cc_start: 0.8256 (tp) cc_final: 0.8055 (tp) REVERT: I 60 ASP cc_start: 0.8570 (t0) cc_final: 0.8155 (t0) REVERT: J 13 ASN cc_start: 0.8031 (m110) cc_final: 0.7720 (m-40) REVERT: K 40 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: L 76 GLU cc_start: 0.7942 (pp20) cc_final: 0.7686 (pp20) REVERT: M 14 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7711 (tm-30) REVERT: N 20 ASP cc_start: 0.8026 (t0) cc_final: 0.7808 (t0) REVERT: O 31 ARG cc_start: 0.8096 (mmt180) cc_final: 0.7796 (mmp80) outliers start: 59 outliers final: 43 residues processed: 463 average time/residue: 0.1134 time to fit residues: 72.5324 Evaluate side-chains 459 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 413 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [19, 127, 103, 50, 76, 100, 31, 112, 110, 137, 132] chunk 19 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN E 51 HIS F 61 GLN F 71 HIS I 30 HIS K 13 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.120011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094999 restraints weight = 28993.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094278 restraints weight = 20978.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095427 restraints weight = 20324.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095711 restraints weight = 14128.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095991 restraints weight = 13428.503| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12677 Z= 0.165 Angle : 0.851 13.179 17060 Z= 0.432 Chirality : 0.046 0.306 1873 Planarity : 0.004 0.041 2183 Dihedral : 6.315 80.785 1728 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.29 % Allowed : 27.37 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1531 helix: 1.45 (0.16), residues: 1051 sheet: -0.95 (0.53), residues: 93 loop : -1.58 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 197 TYR 0.022 0.001 TYR J 67 PHE 0.025 0.001 PHE A 81 TRP 0.020 0.001 TRP B 244 HIS 0.014 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (12651) covalent geometry : angle 0.83780 / 0.43 (17008) SS BOND : bond 0.00514 / 0.35 ( 26) SS BOND : angle 2.86043 / 1.74 ( 52) hydrogen bonds : bond 0.04733 / 3.17 ( 876) hydrogen bonds : angle 4.51609 / 3.33 ( 2592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 437 time to evaluate : 0.458 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7749 (tp-100) REVERT: A 72 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7648 (mttp) REVERT: B 107 LYS cc_start: 0.8177 (mttm) cc_final: 0.7830 (mttm) REVERT: B 241 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8348 (mp) REVERT: D 23 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9145 (mttt) REVERT: D 39 ARG cc_start: 0.8386 (ttp80) cc_final: 0.7951 (tpt90) REVERT: E 27 THR cc_start: 0.9228 (p) cc_final: 0.8988 (t) REVERT: E 50 GLU cc_start: 0.8543 (tp30) cc_final: 0.8158 (tp30) REVERT: E 62 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7859 (ttt90) REVERT: G 14 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7915 (mm-30) REVERT: G 20 ASP cc_start: 0.7865 (t70) cc_final: 0.7611 (t0) REVERT: G 21 MET cc_start: 0.8551 (tmm) cc_final: 0.8139 (tmm) REVERT: G 31 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8695 (ttm-80) REVERT: H 31 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.7917 (mtm-85) REVERT: L 76 GLU cc_start: 0.7926 (pp20) cc_final: 0.7689 (pp20) REVERT: N 20 ASP cc_start: 0.8030 (t0) cc_final: 0.7778 (t0) outliers start: 57 outliers final: 43 residues processed: 462 average time/residue: 0.1170 time to fit residues: 74.8375 Evaluate side-chains 455 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 411 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [41, 1, 129, 115, 78, 97, 80, 101, 25, 37, 11] chunk 41 optimal weight: 0.0570 chunk 1 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN C 191 HIS E 51 HIS ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN K 13 GLN ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.119981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094664 restraints weight = 29351.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094062 restraints weight = 20901.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094762 restraints weight = 21755.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.096256 restraints weight = 15650.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.096116 restraints weight = 12476.161| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12677 Z= 0.168 Angle : 0.883 13.475 17060 Z= 0.448 Chirality : 0.047 0.297 1873 Planarity : 0.004 0.036 2183 Dihedral : 6.175 80.283 1728 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.06 % Allowed : 27.89 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.22), residues: 1531 helix: 1.44 (0.16), residues: 1050 sheet: -0.92 (0.53), residues: 93 loop : -1.51 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 31 TYR 0.023 0.001 TYR J 67 PHE 0.029 0.001 PHE A 81 TRP 0.031 0.001 TRP B 244 HIS 0.014 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (12651) covalent geometry : angle 0.86923 / 0.44 (17008) SS BOND : bond 0.00703 / 0.45 ( 26) SS BOND : angle 2.90366 / 1.78 ( 52) hydrogen bonds : bond 0.04792 / 3.19 ( 876) hydrogen bonds : angle 4.55942 / 3.36 ( 2592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 432 time to evaluate : 0.463 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: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7757 (mttp) REVERT: B 163 THR cc_start: 0.8810 (p) cc_final: 0.8602 (t) REVERT: B 241 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8313 (mp) REVERT: D 39 ARG cc_start: 0.8384 (ttp80) cc_final: 0.7849 (tpt90) REVERT: E 17 PHE cc_start: 0.7169 (m-80) cc_final: 0.6961 (m-80) REVERT: E 50 GLU cc_start: 0.8568 (tp30) cc_final: 0.8202 (tp30) REVERT: E 62 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7884 (ttt90) REVERT: G 20 ASP cc_start: 0.8125 (t70) cc_final: 0.7910 (t0) REVERT: L 76 GLU cc_start: 0.7901 (pp20) cc_final: 0.7624 (pp20) REVERT: N 20 ASP cc_start: 0.8000 (t0) cc_final: 0.7749 (t0) outliers start: 54 outliers final: 45 residues processed: 457 average time/residue: 0.1173 time to fit residues: 73.9792 Evaluate side-chains 455 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 409 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 HIS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [136, 63, 3, 35, 54, 55, 34, 81, 21, 92, 93] chunk 136 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.114721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.088474 restraints weight = 28709.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088393 restraints weight = 17785.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089178 restraints weight = 16512.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089898 restraints weight = 12332.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.090088 restraints weight = 11153.681| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12677 Z= 0.176 Angle : 0.927 13.547 17060 Z= 0.470 Chirality : 0.048 0.312 1873 Planarity : 0.005 0.096 2183 Dihedral : 6.010 80.385 1728 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.38 % Allowed : 29.32 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1531 helix: 1.37 (0.16), residues: 1059 sheet: -0.80 (0.51), residues: 105 loop : -1.55 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 31 TYR 0.025 0.001 TYR J 67 PHE 0.028 0.001 PHE A 81 TRP 0.032 0.001 TRP B 244 HIS 0.018 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (12651) covalent geometry : angle 0.91509 / 0.46 (17008) SS BOND : bond 0.00524 / 0.36 ( 26) SS BOND : angle 2.79280 / 1.73 ( 52) hydrogen bonds : bond 0.04793 / 3.18 ( 876) hydrogen bonds : angle 4.61093 / 3.40 ( 2592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 426 time to evaluate : 0.466 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: A 40 ARG cc_start: 0.7207 (tpp-160) cc_final: 0.7004 (tpp-160) REVERT: A 59 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7864 (tp40) REVERT: A 72 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7664 (mttp) REVERT: B 57 ASN cc_start: 0.8005 (p0) cc_final: 0.7772 (p0) REVERT: B 241 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8328 (mp) REVERT: D 39 ARG cc_start: 0.8487 (ttp80) cc_final: 0.7971 (tpt90) REVERT: E 17 PHE cc_start: 0.7231 (m-80) cc_final: 0.6965 (m-80) REVERT: E 50 GLU cc_start: 0.8845 (tp30) cc_final: 0.8417 (tp30) REVERT: E 62 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8078 (ttt90) REVERT: F 65 MET cc_start: 0.8514 (ptp) cc_final: 0.8230 (ptp) REVERT: F 66 ARG cc_start: 0.8824 (tpp-160) cc_final: 0.8508 (tpp-160) REVERT: F 71 HIS cc_start: 0.6455 (m-70) cc_final: 0.6216 (m-70) REVERT: G 20 ASP cc_start: 0.8317 (t70) cc_final: 0.7986 (t0) REVERT: G 31 ARG cc_start: 0.9149 (ttm-80) cc_final: 0.8904 (ttm-80) REVERT: G 72 LEU cc_start: 0.8663 (mt) cc_final: 0.8463 (mt) REVERT: H 25 MET cc_start: 0.8652 (ptm) cc_final: 0.8399 (ptm) REVERT: I 22 TYR cc_start: 0.8610 (t80) cc_final: 0.8355 (t80) REVERT: J 23 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8323 (mtm110) REVERT: L 62 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8018 (ttt-90) REVERT: L 76 GLU cc_start: 0.8091 (pp20) cc_final: 0.7831 (pp20) REVERT: N 20 ASP cc_start: 0.8328 (t0) cc_final: 0.8115 (t0) REVERT: O 42 GLU cc_start: 0.7464 (tp30) cc_final: 0.7214 (tp30) outliers start: 45 outliers final: 37 residues processed: 449 average time/residue: 0.1180 time to fit residues: 73.2795 Evaluate side-chains 450 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 412 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 65 MET Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 16 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: [48, 65, 45, 33, 17, 118, 130, 150, 99, 88, 120] chunk 48 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 33 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 HIS D 54 GLN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.120049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095074 restraints weight = 29473.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.093397 restraints weight = 20882.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094394 restraints weight = 20600.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095058 restraints weight = 15402.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095254 restraints weight = 14103.764| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12677 Z= 0.179 Angle : 0.936 16.338 17060 Z= 0.476 Chirality : 0.048 0.290 1873 Planarity : 0.004 0.049 2183 Dihedral : 5.976 80.325 1728 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.23 % Allowed : 29.55 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.22), residues: 1531 helix: 1.41 (0.16), residues: 1051 sheet: -0.93 (0.51), residues: 105 loop : -1.51 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 66 TYR 0.028 0.002 TYR I 58 PHE 0.029 0.001 PHE A 81 TRP 0.030 0.001 TRP B 244 HIS 0.017 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (12651) covalent geometry : angle 0.92350 / 0.47 (17008) SS BOND : bond 0.00557 / 0.38 ( 26) SS BOND : angle 2.90844 / 1.95 ( 52) hydrogen bonds : bond 0.04866 / 3.21 ( 876) hydrogen bonds : angle 4.65001 / 3.44 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2420.88 seconds wall clock time: 42 minutes 32.67 seconds (2552.67 seconds total)