Starting phenix.real_space_refine on Thu Sep 18 00:22:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cgp_9958/09_2025/7cgp_9958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgp_9958/09_2025/7cgp_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_9958/09_2025/7cgp_9958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgp_9958/09_2025/7cgp_9958.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgp_9958/09_2025/7cgp_9958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgp_9958/09_2025/7cgp_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-2.0-5805/lib/python3.9/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: 3.32, per 1000 atoms: 0.27 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: 1.20 Conformation dependent library (CDL) restraints added in 665.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.36 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: 2.24 Time building geometry restraints manager: 1.57 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 - 30.79: 7562 30.79 - 61.58: 262 61.58 - 92.37: 25 92.37 - 123.16: 2 123.16 - 153.96: 3 Dihedral angle restraints: 7854 sinusoidal: 3274 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=" C4 PEE C 301 " pdb=" O4P PEE C 301 " pdb=" P PEE C 301 " pdb=" O1P PEE C 301 " ideal model delta sinusoidal sigma weight residual 57.28 -148.76 -153.96 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C3 PEE C 301 " pdb=" C1 PEE C 301 " pdb=" C2 PEE C 301 " pdb=" O3P PEE C 301 " ideal model delta sinusoidal sigma weight residual 62.73 -82.54 145.27 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7851 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: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 15.247 153.956 4800 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 aren 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 covalent geometry : bond 0.00611 (12651) covalent geometry : angle 0.65908 (17008) SS BOND : bond 0.00400 ( 26) SS BOND : angle 1.51254 ( 52) hydrogen bonds : bond 0.13426 ( 876) hydrogen bonds : angle 5.89083 ( 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 : 0.531 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: 0.1538 time to fit residues: 119.8506 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 : 0.613 ------------------------------------------------------------------------------- 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: 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3915 r_free = 0.3915 target = 0.123545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.098449 restraints weight = 28941.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097847 restraints weight = 18710.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098968 restraints weight = 18478.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099199 restraints weight = 12964.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099309 restraints weight = 12894.877| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12677 Z= 0.170 Angle : 0.768 12.252 17060 Z= 0.394 Chirality : 0.044 0.291 1873 Planarity : 0.005 0.052 2183 Dihedral : 10.299 155.755 1744 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.86 % Allowed : 18.12 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.21), residues: 1531 helix: 0.80 (0.16), residues: 1056 sheet: -2.19 (0.41), residues: 115 loop : -2.52 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 104 TYR 0.018 0.002 TYR C 124 PHE 0.023 0.001 PHE A 81 TRP 0.014 0.002 TRP B 28 HIS 0.011 0.001 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00382 (12651) covalent geometry : angle 0.75079 (17008) SS BOND : bond 0.00564 ( 26) SS BOND : angle 3.03892 ( 52) hydrogen bonds : bond 0.05012 ( 876) hydrogen bonds : angle 4.63263 ( 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 525 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 487 time to evaluate : 0.526 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: A 140 GLU cc_start: 0.8426 (pp20) cc_final: 0.7768 (tp30) REVERT: B 241 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 329 ASP cc_start: 0.6402 (p0) cc_final: 0.5942 (p0) REVERT: B 390 TYR cc_start: 0.8027 (m-80) cc_final: 0.7821 (m-10) REVERT: C 76 LEU cc_start: 0.6678 (tp) cc_final: 0.6417 (pp) REVERT: C 134 TYR cc_start: 0.8810 (p90) cc_final: 0.8582 (p90) REVERT: C 143 SER cc_start: 0.9048 (t) cc_final: 0.8536 (t) REVERT: C 214 ASP cc_start: 0.7858 (m-30) cc_final: 0.7574 (m-30) REVERT: C 218 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8240 (tmtt) REVERT: F 20 THR cc_start: 0.9127 (p) cc_final: 0.8881 (t) REVERT: F 35 ASP cc_start: 0.8358 (p0) cc_final: 0.7971 (p0) REVERT: F 62 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.6386 (ttm-80) REVERT: F 66 ARG cc_start: 0.8699 (tpp-160) cc_final: 0.8322 (mpp-170) REVERT: G 13 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.7863 (tp) REVERT: G 20 ASP cc_start: 0.8070 (t70) cc_final: 0.7779 (t0) REVERT: G 31 ARG cc_start: 0.9150 (ttm-80) cc_final: 0.8596 (ttm-80) REVERT: G 42 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7245 (mm-30) REVERT: H 25 MET cc_start: 0.8646 (ptm) cc_final: 0.8434 (ptm) REVERT: H 49 VAL cc_start: 0.8822 (t) cc_final: 0.8597 (p) REVERT: H 64 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8113 (ttm-80) REVERT: I 14 GLU cc_start: 0.8584 (tp30) cc_final: 0.8324 (tp30) REVERT: I 17 MET cc_start: 0.8503 (tpt) cc_final: 0.8266 (tmm) REVERT: I 21 MET cc_start: 0.8860 (tmm) cc_final: 0.8091 (tmm) REVERT: I 25 MET cc_start: 0.7905 (ptp) cc_final: 0.7274 (ptm) REVERT: I 58 TYR cc_start: 0.8105 (t80) cc_final: 0.7693 (t80) REVERT: I 60 ASP cc_start: 0.8469 (t0) cc_final: 0.8181 (t0) REVERT: I 64 ARG cc_start: 0.8214 (ptm-80) cc_final: 0.7862 (ptm-80) REVERT: J 9 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7687 (tp40) REVERT: L 69 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7423 (tm-30) REVERT: O 16 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6977 (mt-10) REVERT: O 42 GLU cc_start: 0.7718 (tp30) cc_final: 0.7026 (tp30) outliers start: 38 outliers final: 21 residues processed: 497 average time/residue: 0.1488 time to fit residues: 99.1774 Evaluate side-chains 436 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 413 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 71 HIS 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 Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain N residue 12 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN E 51 HIS E 54 GLN F 51 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 ASN K 71 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.121567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.096529 restraints weight = 29232.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095583 restraints weight = 20152.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.096784 restraints weight = 19481.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.097070 restraints weight = 13941.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.097189 restraints weight = 13541.297| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 12677 Z= 0.167 Angle : 0.755 11.540 17060 Z= 0.388 Chirality : 0.043 0.246 1873 Planarity : 0.004 0.041 2183 Dihedral : 9.766 154.758 1740 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.36 % Allowed : 20.60 % Favored : 75.04 % 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 aren not related in a simple way. whole: 0.32 (0.22), residues: 1531 helix: 1.18 (0.16), residues: 1063 sheet: -1.65 (0.44), residues: 109 loop : -2.05 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 104 TYR 0.019 0.001 TYR A 31 PHE 0.018 0.001 PHE A 81 TRP 0.012 0.001 TRP B 244 HIS 0.007 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00384 (12651) covalent geometry : angle 0.74170 (17008) SS BOND : bond 0.00463 ( 26) SS BOND : angle 2.68573 ( 52) hydrogen bonds : bond 0.04820 ( 876) hydrogen bonds : angle 4.51288 ( 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 506 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 448 time to evaluate : 0.552 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: A 59 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7390 (tp40) REVERT: A 140 GLU cc_start: 0.8413 (pp20) cc_final: 0.7839 (tp30) REVERT: B 107 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8078 (mttm) REVERT: B 241 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8508 (mp) REVERT: B 329 ASP cc_start: 0.6518 (p0) cc_final: 0.5973 (p0) REVERT: B 359 HIS cc_start: 0.6632 (m-70) cc_final: 0.6431 (m-70) REVERT: C 134 TYR cc_start: 0.8873 (p90) cc_final: 0.8641 (p90) REVERT: C 143 SER cc_start: 0.9107 (t) cc_final: 0.8632 (t) REVERT: C 179 MET cc_start: 0.8354 (mmm) cc_final: 0.8076 (mmm) REVERT: C 218 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8294 (tmtt) REVERT: D 17 PHE cc_start: 0.8745 (t80) cc_final: 0.8400 (t80) REVERT: D 18 LEU cc_start: 0.8391 (mt) cc_final: 0.8064 (pp) REVERT: D 53 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8217 (mm) REVERT: F 50 GLU cc_start: 0.7754 (pt0) cc_final: 0.7452 (tm-30) REVERT: F 62 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.6649 (ttm-80) REVERT: F 66 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8414 (mpp-170) REVERT: G 20 ASP cc_start: 0.8155 (t70) cc_final: 0.7864 (t0) REVERT: G 31 ARG cc_start: 0.9127 (ttm-80) cc_final: 0.8657 (ttm-80) REVERT: G 42 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7260 (mm-30) REVERT: H 31 ARG cc_start: 0.8749 (mtm-85) cc_final: 0.8392 (mtm-85) REVERT: H 60 ASP cc_start: 0.8616 (t0) cc_final: 0.8350 (t0) REVERT: I 21 MET cc_start: 0.8784 (tmm) cc_final: 0.7921 (tmm) REVERT: I 25 MET cc_start: 0.8057 (ptp) cc_final: 0.7685 (ptp) REVERT: I 58 TYR cc_start: 0.8209 (t80) cc_final: 0.7707 (t80) REVERT: J 74 LEU cc_start: 0.8830 (tp) cc_final: 0.8294 (tp) REVERT: K 58 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7808 (mtpp) REVERT: K 71 HIS cc_start: 0.6967 (OUTLIER) cc_final: 0.6688 (m90) REVERT: L 69 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7582 (tm-30) REVERT: N 8 GLN cc_start: 0.8246 (pt0) cc_final: 0.7823 (pm20) REVERT: N 14 GLU cc_start: 0.5757 (mm-30) cc_final: 0.5521 (mm-30) REVERT: N 17 MET cc_start: 0.8416 (ttp) cc_final: 0.8140 (ttp) outliers start: 58 outliers final: 31 residues processed: 476 average time/residue: 0.1371 time to fit residues: 88.3333 Evaluate side-chains 434 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 400 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 75 VAL 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 L residue 7 GLU Chi-restraints excluded: chain L residue 28 CYS Chi-restraints excluded: chain L residue 59 MET 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: chunk 143 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.0020 chunk 58 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN E 51 HIS F 71 HIS ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 71 HIS O 37 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.120853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095578 restraints weight = 29073.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094677 restraints weight = 19490.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.095770 restraints weight = 19923.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.096070 restraints weight = 14189.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096169 restraints weight = 13776.608| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 12677 Z= 0.164 Angle : 0.770 12.145 17060 Z= 0.391 Chirality : 0.044 0.313 1873 Planarity : 0.004 0.054 2183 Dihedral : 9.555 155.044 1739 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.59 % Allowed : 21.88 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.22), residues: 1531 helix: 1.33 (0.16), residues: 1064 sheet: -1.32 (0.46), residues: 110 loop : -1.91 (0.33), residues: 357 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 0.008 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00379 (12651) covalent geometry : angle 0.75386 (17008) SS BOND : bond 0.00468 ( 26) SS BOND : angle 2.94846 ( 52) hydrogen bonds : bond 0.04747 ( 876) hydrogen bonds : angle 4.42016 ( 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 499 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 438 time to evaluate : 0.543 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: 0.7864 (tp-100) cc_final: 0.7532 (tp-100) REVERT: A 140 GLU cc_start: 0.8377 (pp20) cc_final: 0.7919 (tp30) REVERT: B 107 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8051 (mttm) REVERT: B 241 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8470 (mp) REVERT: C 143 SER cc_start: 0.9172 (t) cc_final: 0.8706 (t) REVERT: C 218 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8340 (tmtt) REVERT: D 17 PHE cc_start: 0.8782 (t80) cc_final: 0.8443 (t80) REVERT: D 18 LEU cc_start: 0.8468 (mt) cc_final: 0.8160 (pp) REVERT: E 27 THR cc_start: 0.9314 (p) cc_final: 0.9094 (t) REVERT: E 55 LYS cc_start: 0.8306 (ptpp) cc_final: 0.8049 (ptpp) REVERT: F 50 GLU cc_start: 0.7842 (pt0) cc_final: 0.7416 (tm-30) REVERT: F 62 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7341 (ttm-80) REVERT: F 66 ARG cc_start: 0.8742 (tpp-160) cc_final: 0.8279 (mmt90) REVERT: G 20 ASP cc_start: 0.8085 (t70) cc_final: 0.7844 (t0) REVERT: G 31 ARG cc_start: 0.9124 (ttm-80) cc_final: 0.8827 (ttm-80) REVERT: G 42 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7294 (mm-30) REVERT: H 31 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8397 (mtm-85) REVERT: I 21 MET cc_start: 0.8734 (tmm) cc_final: 0.7860 (tmm) REVERT: I 25 MET cc_start: 0.8040 (ptp) cc_final: 0.7572 (ptp) REVERT: I 43 LEU cc_start: 0.8223 (tp) cc_final: 0.8008 (tp) REVERT: I 58 TYR cc_start: 0.8216 (t80) cc_final: 0.7669 (t80) REVERT: I 64 ARG cc_start: 0.7983 (ptm-80) cc_final: 0.7680 (ptm-80) REVERT: J 9 GLN cc_start: 0.8262 (tp40) cc_final: 0.7880 (tp40) REVERT: K 31 ASP cc_start: 0.8773 (m-30) cc_final: 0.8559 (m-30) REVERT: K 40 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: L 69 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7717 (tm-30) REVERT: N 17 MET cc_start: 0.8341 (ttp) cc_final: 0.8120 (ttp) REVERT: N 20 ASP cc_start: 0.7988 (t0) cc_final: 0.7767 (t0) outliers start: 61 outliers final: 34 residues processed: 468 average time/residue: 0.1290 time to fit residues: 83.3734 Evaluate side-chains 438 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 402 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 40 GLU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain M residue 52 ASP 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: chunk 116 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN E 51 HIS E 54 GLN F 71 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN M 62 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.120397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094763 restraints weight = 29053.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.094300 restraints weight = 20044.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095028 restraints weight = 20846.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.096531 restraints weight = 15194.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.096425 restraints weight = 12159.094| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5285 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= 0.161 Angle : 0.752 13.680 17060 Z= 0.381 Chirality : 0.044 0.332 1873 Planarity : 0.004 0.049 2183 Dihedral : 9.309 154.755 1739 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.49 % Allowed : 22.11 % Favored : 72.41 % 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 aren not related in a simple way. whole: 0.76 (0.22), residues: 1531 helix: 1.47 (0.16), residues: 1060 sheet: -1.13 (0.46), residues: 110 loop : -1.85 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 64 TYR 0.019 0.001 TYR J 67 PHE 0.021 0.001 PHE E 29 TRP 0.014 0.001 TRP B 244 HIS 0.011 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00371 (12651) covalent geometry : angle 0.74249 (17008) SS BOND : bond 0.00426 ( 26) SS BOND : angle 2.32569 ( 52) hydrogen bonds : bond 0.04631 ( 876) hydrogen bonds : angle 4.35176 ( 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 508 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 435 time to evaluate : 0.591 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: 0.7988 (tp-100) cc_final: 0.7622 (tp-100) REVERT: B 107 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8192 (mttm) REVERT: B 113 MET cc_start: 0.8257 (ttm) cc_final: 0.8027 (ttm) REVERT: B 241 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8445 (mp) REVERT: B 310 THR cc_start: 0.7962 (t) cc_final: 0.7489 (t) REVERT: C 143 SER cc_start: 0.9208 (t) cc_final: 0.8770 (t) REVERT: C 218 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8366 (tmtt) REVERT: D 17 PHE cc_start: 0.8753 (t80) cc_final: 0.8423 (t80) REVERT: D 18 LEU cc_start: 0.8492 (mt) cc_final: 0.8203 (pp) REVERT: D 23 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9103 (mttt) REVERT: E 27 THR cc_start: 0.9275 (p) cc_final: 0.9030 (t) REVERT: F 50 GLU cc_start: 0.7825 (pt0) cc_final: 0.7331 (tm-30) REVERT: F 66 ARG cc_start: 0.8774 (tpp-160) cc_final: 0.8388 (mpt-90) REVERT: G 14 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7729 (mm-30) REVERT: G 20 ASP cc_start: 0.8151 (t70) cc_final: 0.7874 (t0) REVERT: G 22 TYR cc_start: 0.9076 (t80) cc_final: 0.8581 (t80) REVERT: G 31 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8843 (ttm-80) REVERT: H 31 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8388 (mtm-85) REVERT: H 68 LYS cc_start: 0.8909 (tppt) cc_final: 0.8702 (tppt) REVERT: I 21 MET cc_start: 0.8712 (tmm) cc_final: 0.8198 (tmm) REVERT: I 25 MET cc_start: 0.8035 (ptp) cc_final: 0.7824 (ptm) REVERT: I 43 LEU cc_start: 0.8116 (tp) cc_final: 0.7884 (tp) REVERT: J 12 ARG cc_start: 0.7752 (mtp180) cc_final: 0.7428 (mtm-85) REVERT: L 69 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7859 (tm-30) REVERT: N 14 GLU cc_start: 0.5764 (mm-30) cc_final: 0.5447 (mm-30) REVERT: N 17 MET cc_start: 0.8379 (ttp) cc_final: 0.8157 (ttp) REVERT: O 5 ARG cc_start: 0.8083 (ptt-90) cc_final: 0.7870 (ptt-90) outliers start: 73 outliers final: 43 residues processed: 468 average time/residue: 0.1264 time to fit residues: 81.3165 Evaluate side-chains 446 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 402 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 192 LEU 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 E residue 59 MET Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 65 MET 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 79 ILE Chi-restraints excluded: chain K residue 13 GLN 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 L residue 7 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 52 CYS Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain N residue 31 ARG 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: chunk 49 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 111 optimal weight: 0.0980 chunk 115 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS F 71 HIS ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.117922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.092800 restraints weight = 28974.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.091481 restraints weight = 20927.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092683 restraints weight = 22374.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093077 restraints weight = 15140.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093321 restraints weight = 14171.824| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 12677 Z= 0.208 Angle : 0.821 15.291 17060 Z= 0.418 Chirality : 0.046 0.283 1873 Planarity : 0.004 0.043 2183 Dihedral : 9.190 152.848 1738 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.11 % Allowed : 23.53 % Favored : 71.35 % 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 aren not related in a simple way. whole: 0.72 (0.22), residues: 1531 helix: 1.43 (0.16), residues: 1052 sheet: -1.15 (0.54), residues: 86 loop : -1.74 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 64 TYR 0.020 0.002 TYR H 22 PHE 0.024 0.002 PHE E 29 TRP 0.014 0.002 TRP B 244 HIS 0.007 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00495 (12651) covalent geometry : angle 0.80245 (17008) SS BOND : bond 0.00521 ( 26) SS BOND : angle 3.21558 ( 52) hydrogen bonds : bond 0.04884 ( 876) hydrogen bonds : angle 4.47832 ( 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 494 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 426 time to evaluate : 0.984 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: 0.8082 (tp-100) cc_final: 0.7676 (tp-100) REVERT: A 72 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7765 (mttp) REVERT: B 177 ASP cc_start: 0.7610 (t70) cc_final: 0.7398 (t70) REVERT: B 241 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8420 (mp) REVERT: C 218 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8406 (tmtt) REVERT: D 17 PHE cc_start: 0.8752 (t80) cc_final: 0.8456 (t80) REVERT: D 23 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9098 (mttt) REVERT: D 59 MET cc_start: 0.8507 (ttp) cc_final: 0.8303 (ttp) REVERT: E 51 HIS cc_start: 0.7575 (m90) cc_final: 0.6951 (m170) REVERT: E 55 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7921 (ptpp) REVERT: F 50 GLU cc_start: 0.7877 (pt0) cc_final: 0.7324 (tm-30) REVERT: F 66 ARG cc_start: 0.8768 (tpp-160) cc_final: 0.8352 (mpt-90) REVERT: G 20 ASP cc_start: 0.8179 (t70) cc_final: 0.7922 (t0) REVERT: G 31 ARG cc_start: 0.9130 (ttm-80) cc_final: 0.8863 (ttm-80) REVERT: H 18 MET cc_start: 0.8257 (mmp) cc_final: 0.8034 (mmm) REVERT: I 43 LEU cc_start: 0.8196 (tp) cc_final: 0.7994 (tp) REVERT: L 69 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7887 (tm-30) outliers start: 68 outliers final: 50 residues processed: 460 average time/residue: 0.1386 time to fit residues: 87.4614 Evaluate side-chains 449 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 398 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 192 LEU Chi-restraints excluded: chain C residue 217 TYR 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 E residue 59 MET Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 46 THR 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 52 ASP Chi-restraints excluded: chain I residue 65 MET 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 79 ILE 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 24 LEU Chi-restraints excluded: chain L residue 30 LEU 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 M residue 52 ASP Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG 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: chunk 134 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** 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 = 0.3840 r_free = 0.3840 target = 0.118592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093638 restraints weight = 29202.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092753 restraints weight = 20942.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093929 restraints weight = 20604.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094187 restraints weight = 13883.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094460 restraints weight = 13360.541| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12677 Z= 0.171 Angle : 0.839 14.998 17060 Z= 0.425 Chirality : 0.046 0.356 1873 Planarity : 0.004 0.042 2183 Dihedral : 9.021 152.301 1738 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.66 % Allowed : 25.71 % 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 aren not related in a simple way. whole: 0.85 (0.22), residues: 1531 helix: 1.52 (0.16), residues: 1045 sheet: -1.07 (0.53), residues: 88 loop : -1.61 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 197 TYR 0.018 0.001 TYR I 58 PHE 0.028 0.001 PHE A 81 TRP 0.018 0.001 TRP B 244 HIS 0.007 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00402 (12651) covalent geometry : angle 0.82387 (17008) SS BOND : bond 0.00550 ( 26) SS BOND : angle 2.95485 ( 52) hydrogen bonds : bond 0.04868 ( 876) hydrogen bonds : angle 4.46703 ( 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 491 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 429 time to evaluate : 0.573 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: A 72 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7757 (mttp) REVERT: A 140 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7907 (tp30) REVERT: A 154 ASN cc_start: 0.8194 (m110) cc_final: 0.7984 (m-40) REVERT: B 163 THR cc_start: 0.8849 (p) cc_final: 0.8644 (t) REVERT: B 177 ASP cc_start: 0.7615 (t70) cc_final: 0.7392 (t70) REVERT: B 241 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 23 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9093 (mttt) REVERT: E 27 THR cc_start: 0.9238 (p) cc_final: 0.8999 (t) REVERT: E 51 HIS cc_start: 0.7469 (m90) cc_final: 0.7137 (m170) REVERT: F 50 GLU cc_start: 0.7820 (pt0) cc_final: 0.7240 (tm-30) REVERT: G 14 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7670 (mm-30) REVERT: G 20 ASP cc_start: 0.8116 (t70) cc_final: 0.7843 (t0) REVERT: G 22 TYR cc_start: 0.9066 (t80) cc_final: 0.8721 (t80) REVERT: G 31 ARG cc_start: 0.9088 (ttm-80) cc_final: 0.8855 (ttm-80) REVERT: L 69 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7917 (tm-30) outliers start: 62 outliers final: 47 residues processed: 459 average time/residue: 0.1390 time to fit residues: 87.3357 Evaluate side-chains 450 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 198 VAL Chi-restraints excluded: chain C residue 217 TYR 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 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 20 ASP 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 65 MET 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 24 LEU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 56 SER 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: chunk 19 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 76 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS I 30 HIS K 13 GLN L 54 GLN ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3840 r_free = 0.3840 target = 0.118737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093569 restraints weight = 29171.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.092857 restraints weight = 20707.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.093993 restraints weight = 20484.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094176 restraints weight = 14044.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094412 restraints weight = 13870.394| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.6010 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= 0.182 Angle : 0.880 14.641 17060 Z= 0.445 Chirality : 0.046 0.225 1873 Planarity : 0.004 0.041 2183 Dihedral : 8.921 150.918 1738 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.74 % Allowed : 26.84 % Favored : 68.42 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1531 helix: 1.47 (0.16), residues: 1051 sheet: -1.03 (0.52), residues: 93 loop : -1.58 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 31 TYR 0.022 0.002 TYR J 67 PHE 0.032 0.002 PHE E 29 TRP 0.019 0.001 TRP B 244 HIS 0.008 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00428 (12651) covalent geometry : angle 0.86622 (17008) SS BOND : bond 0.00593 ( 26) SS BOND : angle 2.91654 ( 52) hydrogen bonds : bond 0.04978 ( 876) hydrogen bonds : angle 4.55057 ( 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 484 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 421 time to evaluate : 0.543 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 67 GLU cc_start: 0.7824 (pp20) cc_final: 0.7566 (pp20) REVERT: A 72 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7815 (mttp) REVERT: A 144 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: B 177 ASP cc_start: 0.7662 (t70) cc_final: 0.7440 (t70) REVERT: B 241 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 216 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8455 (ttmt) REVERT: D 23 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9113 (mttt) REVERT: G 17 MET cc_start: 0.8225 (ppp) cc_final: 0.7391 (ppp) REVERT: G 20 ASP cc_start: 0.8147 (t70) cc_final: 0.7841 (t0) REVERT: I 64 ARG cc_start: 0.8332 (ptm-80) cc_final: 0.7810 (ptm-80) REVERT: K 58 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7427 (mtmt) REVERT: L 69 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7988 (tm-30) REVERT: O 59 LEU cc_start: 0.8752 (mt) cc_final: 0.8418 (mt) outliers start: 63 outliers final: 50 residues processed: 453 average time/residue: 0.1400 time to fit residues: 87.6015 Evaluate side-chains 463 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 410 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 160 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 335 ILE 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 216 LYS 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 59 MET 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 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 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 65 MET 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 24 LEU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 56 SER 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: chunk 41 optimal weight: 0.0000 chunk 1 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 25 optimal weight: 0.0570 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.120002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094165 restraints weight = 29335.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092491 restraints weight = 19214.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.093684 restraints weight = 20659.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094045 restraints weight = 15071.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094288 restraints weight = 14033.515| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12677 Z= 0.172 Angle : 0.910 16.399 17060 Z= 0.454 Chirality : 0.046 0.255 1873 Planarity : 0.004 0.042 2183 Dihedral : 8.764 150.518 1738 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.91 % Allowed : 28.65 % Favored : 67.44 % 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 aren not related in a simple way. whole: 0.81 (0.22), residues: 1531 helix: 1.45 (0.16), residues: 1042 sheet: -0.97 (0.52), residues: 93 loop : -1.51 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 31 TYR 0.022 0.001 TYR J 67 PHE 0.033 0.001 PHE E 29 TRP 0.020 0.001 TRP B 244 HIS 0.004 0.001 HIS O 30 Details of bonding type rmsd covalent geometry : bond 0.00390 (12651) covalent geometry : angle 0.90061 (17008) SS BOND : bond 0.00544 ( 26) SS BOND : angle 2.53012 ( 52) hydrogen bonds : bond 0.04833 ( 876) hydrogen bonds : angle 4.58588 ( 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 487 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 435 time to evaluate : 0.560 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: A 67 GLU cc_start: 0.7921 (pp20) cc_final: 0.7599 (pp20) REVERT: A 72 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7796 (mttp) REVERT: B 57 ASN cc_start: 0.7960 (p0) cc_final: 0.7660 (p0) REVERT: B 241 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8278 (mp) REVERT: C 216 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8331 (ttpp) REVERT: D 23 LYS cc_start: 0.9400 (ttmt) cc_final: 0.9151 (mttt) REVERT: E 17 PHE cc_start: 0.7361 (m-80) cc_final: 0.7150 (m-80) REVERT: G 17 MET cc_start: 0.8386 (ppp) cc_final: 0.8164 (ppp) REVERT: G 20 ASP cc_start: 0.8083 (t70) cc_final: 0.7745 (t0) REVERT: G 22 TYR cc_start: 0.9077 (t80) cc_final: 0.8738 (t80) REVERT: I 64 ARG cc_start: 0.8372 (ptm-80) cc_final: 0.7945 (ptm-80) REVERT: L 69 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8088 (tm-30) REVERT: L 76 GLU cc_start: 0.7812 (pp20) cc_final: 0.7540 (pp20) REVERT: O 8 GLN cc_start: 0.8883 (pt0) cc_final: 0.8668 (pt0) outliers start: 52 outliers final: 40 residues processed: 455 average time/residue: 0.1376 time to fit residues: 85.9918 Evaluate side-chains 457 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 416 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 161 ILE Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 49 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 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 48 CYS 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 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 52 ASP Chi-restraints excluded: chain I residue 65 MET 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 71 HIS Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 52 ASP 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: chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 35 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 54 GLN ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.120408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095430 restraints weight = 29600.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093943 restraints weight = 19543.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095125 restraints weight = 20411.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095460 restraints weight = 14589.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095731 restraints weight = 13789.102| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12677 Z= 0.173 Angle : 0.928 13.970 17060 Z= 0.465 Chirality : 0.047 0.283 1873 Planarity : 0.004 0.042 2183 Dihedral : 8.688 150.184 1738 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.68 % Allowed : 29.32 % Favored : 66.99 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1531 helix: 1.44 (0.16), residues: 1049 sheet: -0.88 (0.53), residues: 93 loop : -1.49 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 31 TYR 0.022 0.001 TYR J 67 PHE 0.031 0.001 PHE E 29 TRP 0.010 0.001 TRP B 28 HIS 0.007 0.001 HIS O 37 Details of bonding type rmsd covalent geometry : bond 0.00394 (12651) covalent geometry : angle 0.91590 (17008) SS BOND : bond 0.00641 ( 26) SS BOND : angle 2.82592 ( 52) hydrogen bonds : bond 0.04796 ( 876) hydrogen bonds : angle 4.58431 ( 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 487 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 438 time to evaluate : 0.530 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 72 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7751 (mttp) REVERT: B 57 ASN cc_start: 0.7916 (p0) cc_final: 0.7597 (p0) REVERT: B 241 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8458 (mp) REVERT: C 216 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8342 (ttpp) REVERT: D 23 LYS cc_start: 0.9386 (ttmt) cc_final: 0.9179 (mttt) REVERT: D 45 GLU cc_start: 0.8963 (mp0) cc_final: 0.8575 (mp0) REVERT: E 27 THR cc_start: 0.9226 (p) cc_final: 0.9004 (t) REVERT: G 16 GLU cc_start: 0.8321 (pp20) cc_final: 0.8106 (pp20) REVERT: G 20 ASP cc_start: 0.8151 (t70) cc_final: 0.7828 (t0) REVERT: G 72 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8533 (mt) REVERT: I 64 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.7799 (ptm-80) REVERT: J 23 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8248 (mtm110) REVERT: L 69 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8070 (tm-30) REVERT: L 74 GLN cc_start: 0.8634 (tp40) cc_final: 0.8367 (tp40) REVERT: N 20 ASP cc_start: 0.8060 (t0) cc_final: 0.7836 (t0) REVERT: O 63 GLU cc_start: 0.7483 (mp0) cc_final: 0.7179 (mp0) outliers start: 49 outliers final: 41 residues processed: 459 average time/residue: 0.1427 time to fit residues: 89.5448 Evaluate side-chains 459 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 416 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 335 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 48 CYS 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 72 LEU Chi-restraints excluded: chain G residue 74 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 65 MET 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 L residue 48 CYS Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 63 GLU Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain O residue 56 SER 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: chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.119718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095018 restraints weight = 29499.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093257 restraints weight = 21288.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094457 restraints weight = 21363.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094793 restraints weight = 15089.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.095027 restraints weight = 14347.076| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.6418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12677 Z= 0.178 Angle : 0.939 13.907 17060 Z= 0.473 Chirality : 0.048 0.409 1873 Planarity : 0.004 0.048 2183 Dihedral : 8.594 148.785 1738 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.38 % Allowed : 30.75 % Favored : 65.86 % 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 aren not related in a simple way. whole: 0.84 (0.22), residues: 1531 helix: 1.39 (0.16), residues: 1052 sheet: -0.76 (0.52), residues: 103 loop : -1.39 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 64 TYR 0.026 0.002 TYR C 124 PHE 0.029 0.001 PHE E 29 TRP 0.036 0.001 TRP B 244 HIS 0.011 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00417 (12651) covalent geometry : angle 0.92955 (17008) SS BOND : bond 0.00544 ( 26) SS BOND : angle 2.56034 ( 52) hydrogen bonds : bond 0.04758 ( 876) hydrogen bonds : angle 4.59323 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.06 seconds wall clock time: 46 minutes 11.64 seconds (2771.64 seconds total)