Starting phenix.real_space_refine on Wed Jun 11 06:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cgp_9958/06_2025/7cgp_9958.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cgp_9958/06_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_9958/06_2025/7cgp_9958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cgp_9958/06_2025/7cgp_9958.map" model { file = "/net/cci-nas-00/data/ceres_data/7cgp_9958/06_2025/7cgp_9958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cgp_9958/06_2025/7cgp_9958.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP: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: 7.16, per 1000 atoms: 0.58 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: 3.25 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.09 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: 3.17 Time building geometry restraints manager: 3.80 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: 10.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- 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 : 10.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP B 28 HIS 0.012 0.001 HIS O 37 PHE 0.015 0.001 PHE B 80 TYR 0.023 0.002 TYR L 21 ARG 0.008 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.13426 ( 876) hydrogen bonds : angle 5.89083 ( 2592) SS BOND : bond 0.00400 ( 26) SS BOND : angle 1.51254 ( 52) covalent geometry : bond 0.00611 (12651) covalent geometry : angle 0.65908 (17008) *********************** 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 : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.3055 time to fit residues: 237.0458 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 : 1.492 ------------------------------------------------------------------------------- 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 127 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 0.0060 chunk 45 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.122227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096653 restraints weight = 28720.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096168 restraints weight = 18447.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.097096 restraints weight = 18684.710| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12677 Z= 0.181 Angle : 0.772 12.076 17060 Z= 0.397 Chirality : 0.045 0.299 1873 Planarity : 0.005 0.053 2183 Dihedral : 10.289 155.332 1744 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.38 % Allowed : 17.82 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1531 helix: 0.80 (0.16), residues: 1056 sheet: -2.16 (0.41), residues: 114 loop : -2.54 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 28 HIS 0.011 0.001 HIS I 62 PHE 0.023 0.002 PHE A 81 TYR 0.019 0.002 TYR C 124 ARG 0.007 0.001 ARG C 104 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 876) hydrogen bonds : angle 4.65070 ( 2592) SS BOND : bond 0.00645 ( 26) SS BOND : angle 3.07008 ( 52) covalent geometry : bond 0.00413 (12651) covalent geometry : angle 0.75439 (17008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3062 Ramachandran restraints generated. 1531 Oldfield, 0 Emsley, 1531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 481 time to evaluate : 1.616 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: A 140 GLU cc_start: 0.8440 (pp20) cc_final: 0.7770 (tp30) REVERT: B 82 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8360 (mtmm) REVERT: B 241 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 329 ASP cc_start: 0.6506 (p0) cc_final: 0.6058 (p0) REVERT: B 390 TYR cc_start: 0.8047 (m-80) cc_final: 0.7786 (m-10) REVERT: C 76 LEU cc_start: 0.6751 (tp) cc_final: 0.6458 (pp) REVERT: C 134 TYR cc_start: 0.8850 (p90) cc_final: 0.8618 (p90) REVERT: C 143 SER cc_start: 0.9080 (t) cc_final: 0.8568 (t) REVERT: C 214 ASP cc_start: 0.7915 (m-30) cc_final: 0.7644 (m-30) REVERT: C 218 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8207 (tmtt) REVERT: E 62 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8190 (ttt180) REVERT: F 20 THR cc_start: 0.9190 (p) cc_final: 0.8970 (t) REVERT: F 62 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.6414 (ttm-80) REVERT: F 66 ARG cc_start: 0.8715 (tpp-160) cc_final: 0.8327 (mpp-170) REVERT: G 13 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7869 (tp) REVERT: G 20 ASP cc_start: 0.8100 (t70) cc_final: 0.7826 (t0) REVERT: G 31 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8584 (ttm-80) REVERT: G 42 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7289 (mm-30) REVERT: H 49 VAL cc_start: 0.8835 (t) cc_final: 0.8622 (p) REVERT: H 64 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8133 (ttm-80) REVERT: I 14 GLU cc_start: 0.8630 (tp30) cc_final: 0.8335 (tp30) REVERT: I 17 MET cc_start: 0.8505 (tpt) cc_final: 0.8275 (tmm) REVERT: I 21 MET cc_start: 0.8858 (tmm) cc_final: 0.8077 (tmm) REVERT: I 25 MET cc_start: 0.7932 (ptp) cc_final: 0.7278 (ptm) REVERT: I 58 TYR cc_start: 0.8146 (t80) cc_final: 0.7712 (t80) REVERT: I 60 ASP cc_start: 0.8514 (t0) cc_final: 0.8245 (t0) REVERT: I 62 HIS cc_start: 0.7211 (OUTLIER) cc_final: 0.7006 (t-90) REVERT: I 64 ARG cc_start: 0.8157 (ptm-80) cc_final: 0.7690 (ptm-80) REVERT: J 9 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7711 (tp40) REVERT: L 69 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7467 (tm-30) REVERT: M 5 ARG cc_start: 0.6767 (pmt-80) cc_final: 0.6547 (pmt170) REVERT: O 16 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7015 (mt-10) outliers start: 45 outliers final: 24 residues processed: 493 average time/residue: 0.3094 time to fit residues: 204.3251 Evaluate side-chains 440 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 412 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 69 GLU 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 31 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 79 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS E 54 GLN F 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS J 13 ASN K 71 HIS L 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.093923 restraints weight = 28985.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093334 restraints weight = 19951.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094285 restraints weight = 22343.027| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12677 Z= 0.192 Angle : 0.759 12.229 17060 Z= 0.392 Chirality : 0.044 0.220 1873 Planarity : 0.004 0.037 2183 Dihedral : 9.758 154.498 1740 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.19 % Allowed : 20.30 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1531 helix: 1.20 (0.16), residues: 1065 sheet: -1.54 (0.44), residues: 116 loop : -2.20 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 28 HIS 0.014 0.001 HIS K 71 PHE 0.018 0.001 PHE A 81 TYR 0.017 0.002 TYR C 124 ARG 0.007 0.001 ARG J 23 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 876) hydrogen bonds : angle 4.51870 ( 2592) SS BOND : bond 0.00694 ( 26) SS BOND : angle 2.71676 ( 52) covalent geometry : bond 0.00448 (12651) covalent geometry : angle 0.74478 (17008) *********************** 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 529 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 460 time to evaluate : 1.580 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: A 140 GLU cc_start: 0.8422 (pp20) cc_final: 0.7912 (tp30) REVERT: B 82 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8479 (mtmm) REVERT: B 107 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8155 (mttm) REVERT: B 113 MET cc_start: 0.8184 (ttm) cc_final: 0.7944 (ttm) REVERT: B 241 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8510 (mp) REVERT: B 329 ASP cc_start: 0.6778 (p0) cc_final: 0.6314 (p0) REVERT: B 359 HIS cc_start: 0.6599 (m-70) cc_final: 0.6386 (m-70) REVERT: B 390 TYR cc_start: 0.8241 (m-80) cc_final: 0.8025 (m-10) REVERT: C 85 GLU cc_start: 0.7094 (tt0) cc_final: 0.6857 (mt-10) REVERT: C 143 SER cc_start: 0.9209 (t) cc_final: 0.8715 (t) REVERT: C 218 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8339 (tmtt) REVERT: D 39 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8131 (tpt90) REVERT: D 53 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8145 (mm) REVERT: E 27 THR cc_start: 0.9199 (p) cc_final: 0.8986 (t) REVERT: E 62 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8051 (ttt90) REVERT: F 35 ASP cc_start: 0.8313 (p0) cc_final: 0.7931 (p0) REVERT: F 50 GLU cc_start: 0.7605 (pt0) cc_final: 0.7323 (tm-30) REVERT: F 62 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.6656 (ttm-80) REVERT: G 20 ASP cc_start: 0.8205 (t70) cc_final: 0.7915 (t0) REVERT: G 31 ARG cc_start: 0.9115 (ttm-80) cc_final: 0.8686 (ttm-80) REVERT: G 42 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7388 (mm-30) REVERT: H 31 ARG cc_start: 0.8747 (mtm-85) cc_final: 0.8399 (mtm-85) REVERT: H 60 ASP cc_start: 0.8602 (t0) cc_final: 0.8402 (t0) REVERT: I 14 GLU cc_start: 0.8611 (tp30) cc_final: 0.8392 (tp30) REVERT: I 21 MET cc_start: 0.8826 (tmm) cc_final: 0.7925 (tmm) REVERT: I 25 MET cc_start: 0.7963 (ptp) cc_final: 0.7682 (ptp) REVERT: I 58 TYR cc_start: 0.8168 (t80) cc_final: 0.7727 (t80) REVERT: I 64 ARG cc_start: 0.8203 (ptm-80) cc_final: 0.7895 (ptm-80) REVERT: K 40 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: K 58 LYS cc_start: 0.8306 (mmmm) cc_final: 0.7486 (mmmm) REVERT: L 69 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7678 (tm-30) REVERT: N 17 MET cc_start: 0.8383 (ttp) cc_final: 0.8100 (ttp) REVERT: N 20 ASP cc_start: 0.8111 (t0) cc_final: 0.7910 (t0) outliers start: 69 outliers final: 34 residues processed: 496 average time/residue: 0.3207 time to fit residues: 218.1760 Evaluate side-chains 441 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 403 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS 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 253 SER 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 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 62 ARG Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 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 40 GLU Chi-restraints excluded: chain L residue 7 GLU Chi-restraints excluded: chain L residue 28 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 73 GLN Chi-restraints excluded: chain N residue 31 ARG 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 97 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.0010 chunk 124 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 203 GLN E 51 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 22 ASN N 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.121093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.095753 restraints weight = 28581.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094384 restraints weight = 19653.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095628 restraints weight = 19183.915| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12677 Z= 0.156 Angle : 0.776 12.316 17060 Z= 0.394 Chirality : 0.044 0.327 1873 Planarity : 0.004 0.056 2183 Dihedral : 9.530 154.901 1739 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.14 % Allowed : 22.78 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1531 helix: 1.39 (0.16), residues: 1063 sheet: -1.39 (0.45), residues: 112 loop : -1.92 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 244 HIS 0.010 0.001 HIS F 71 PHE 0.024 0.001 PHE A 81 TYR 0.020 0.001 TYR M 38 ARG 0.007 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 876) hydrogen bonds : angle 4.42060 ( 2592) SS BOND : bond 0.00919 ( 26) SS BOND : angle 3.08364 ( 52) covalent geometry : bond 0.00353 (12651) covalent geometry : angle 0.75872 (17008) *********************** 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 506 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 451 time to evaluate : 1.400 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: B 241 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8467 (mp) REVERT: C 134 TYR cc_start: 0.8814 (p90) cc_final: 0.8595 (p90) REVERT: C 143 SER cc_start: 0.9194 (t) cc_final: 0.8751 (t) REVERT: C 218 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8378 (tmtt) REVERT: D 17 PHE cc_start: 0.8779 (t80) cc_final: 0.8556 (t80) REVERT: E 25 THR cc_start: 0.9163 (p) cc_final: 0.8943 (p) REVERT: E 27 THR cc_start: 0.9236 (p) cc_final: 0.8976 (t) REVERT: E 58 LYS cc_start: 0.8814 (ptmt) cc_final: 0.8596 (ptpp) REVERT: E 62 ARG cc_start: 0.8366 (ttt90) cc_final: 0.7916 (ttt90) REVERT: F 42 LYS cc_start: 0.7704 (mttt) cc_final: 0.7183 (mttt) REVERT: F 50 GLU cc_start: 0.7800 (pt0) cc_final: 0.7408 (tm-30) REVERT: F 62 ARG cc_start: 0.8283 (ttm-80) cc_final: 0.7728 (ttm170) REVERT: G 14 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7617 (mm-30) REVERT: G 20 ASP cc_start: 0.8069 (t70) cc_final: 0.7789 (t0) REVERT: G 31 ARG cc_start: 0.9118 (ttm-80) cc_final: 0.8777 (ttm-80) REVERT: G 42 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7404 (mm-30) REVERT: H 31 ARG cc_start: 0.8748 (mtm-85) cc_final: 0.8375 (mtm-85) REVERT: I 14 GLU cc_start: 0.8611 (tp30) cc_final: 0.8394 (tp30) REVERT: I 21 MET cc_start: 0.8774 (tmm) cc_final: 0.7895 (tmm) REVERT: I 25 MET cc_start: 0.7985 (ptp) cc_final: 0.7615 (ptp) REVERT: I 58 TYR cc_start: 0.8189 (t80) cc_final: 0.7803 (t80) REVERT: K 58 LYS cc_start: 0.8175 (mmmm) cc_final: 0.7604 (mmmm) REVERT: L 69 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7688 (tm-30) REVERT: L 76 GLU cc_start: 0.7796 (pp20) cc_final: 0.7550 (pp20) REVERT: N 14 GLU cc_start: 0.5727 (mm-30) cc_final: 0.5525 (mm-30) REVERT: O 5 ARG cc_start: 0.8099 (ptt-90) cc_final: 0.7665 (ptt-90) outliers start: 55 outliers final: 28 residues processed: 474 average time/residue: 0.2866 time to fit residues: 184.4825 Evaluate side-chains 442 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 413 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 186 ASP Chi-restraints excluded: chain C residue 195 HIS 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 F residue 66 ARG Chi-restraints excluded: chain G residue 25 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain H residue 30 HIS Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU 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 O residue 68 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 66 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN E 51 HIS E 54 GLN F 61 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 54 GLN O 37 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.119227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.093540 restraints weight = 28467.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.092391 restraints weight = 18721.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093430 restraints weight = 19800.356| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12677 Z= 0.172 Angle : 0.769 12.518 17060 Z= 0.394 Chirality : 0.044 0.306 1873 Planarity : 0.004 0.049 2183 Dihedral : 9.246 154.194 1739 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.34 % Allowed : 22.33 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1531 helix: 1.49 (0.16), residues: 1058 sheet: -1.32 (0.52), residues: 88 loop : -1.93 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 244 HIS 0.009 0.001 HIS E 51 PHE 0.021 0.001 PHE A 81 TYR 0.021 0.002 TYR H 22 ARG 0.008 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 876) hydrogen bonds : angle 4.37668 ( 2592) SS BOND : bond 0.00611 ( 26) SS BOND : angle 2.57458 ( 52) covalent geometry : bond 0.00397 (12651) covalent geometry : angle 0.75694 (17008) *********************** 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 513 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 442 time to evaluate : 1.928 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 72 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7638 (mttp) REVERT: B 241 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8388 (mt) REVERT: C 218 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8409 (tmtt) REVERT: D 17 PHE cc_start: 0.8750 (t80) cc_final: 0.8496 (t80) REVERT: D 23 LYS cc_start: 0.9414 (ttmt) cc_final: 0.9152 (mttt) REVERT: D 39 ARG cc_start: 0.8532 (ttp80) cc_final: 0.8084 (tpt90) REVERT: E 50 GLU cc_start: 0.8661 (tp30) cc_final: 0.8395 (tp30) REVERT: E 62 ARG cc_start: 0.8374 (ttt90) cc_final: 0.8088 (ttt90) REVERT: F 50 GLU cc_start: 0.8005 (pt0) cc_final: 0.7415 (tm-30) REVERT: F 62 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7779 (ttm170) REVERT: G 20 ASP cc_start: 0.8154 (t70) cc_final: 0.7903 (t0) REVERT: G 31 ARG cc_start: 0.9107 (ttm-80) cc_final: 0.8864 (ttm-80) REVERT: G 42 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7481 (mm-30) REVERT: H 31 ARG cc_start: 0.8745 (mtm-85) cc_final: 0.8405 (mtm-85) REVERT: I 14 GLU cc_start: 0.8656 (tp30) cc_final: 0.8426 (tp30) REVERT: I 21 MET cc_start: 0.8794 (tmm) cc_final: 0.8237 (tmm) REVERT: I 64 ARG cc_start: 0.8229 (ptm-80) cc_final: 0.7575 (ptm-80) REVERT: K 12 LYS cc_start: 0.8338 (mmtm) cc_final: 0.8051 (mmtm) REVERT: K 58 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7990 (mmmm) REVERT: L 69 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7920 (tm-30) REVERT: L 76 GLU cc_start: 0.7836 (pp20) cc_final: 0.7579 (pp20) REVERT: N 20 ASP cc_start: 0.8064 (t0) cc_final: 0.7839 (t0) outliers start: 71 outliers final: 43 residues processed: 479 average time/residue: 0.3775 time to fit residues: 245.7030 Evaluate side-chains 448 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 404 time to evaluate : 1.683 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 195 HIS 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 E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 66 ARG 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 52 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 13 GLN Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 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 28 CYS Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 37 HIS 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 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- 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 51 HIS ** F 71 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.119843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.094519 restraints weight = 29102.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092892 restraints weight = 19371.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094088 restraints weight = 20240.985| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12677 Z= 0.163 Angle : 0.776 12.291 17060 Z= 0.396 Chirality : 0.044 0.302 1873 Planarity : 0.004 0.043 2183 Dihedral : 9.051 154.286 1738 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.51 % Allowed : 24.29 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1531 helix: 1.57 (0.16), residues: 1043 sheet: -1.18 (0.53), residues: 88 loop : -1.78 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 244 HIS 0.012 0.001 HIS E 51 PHE 0.027 0.001 PHE A 81 TYR 0.017 0.001 TYR N 22 ARG 0.008 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 876) hydrogen bonds : angle 4.38649 ( 2592) SS BOND : bond 0.00537 ( 26) SS BOND : angle 2.84669 ( 52) covalent geometry : bond 0.00376 (12651) covalent geometry : angle 0.76144 (17008) *********************** 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 495 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 435 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7665 (mttp) REVERT: A 140 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7799 (tp30) REVERT: A 154 ASN cc_start: 0.8173 (m110) cc_final: 0.7964 (m-40) REVERT: B 241 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8381 (mp) REVERT: C 199 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8407 (t) REVERT: C 218 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8410 (tmtt) REVERT: D 23 LYS cc_start: 0.9409 (ttmt) cc_final: 0.9112 (mttt) REVERT: E 50 GLU cc_start: 0.8659 (tp30) cc_final: 0.8377 (tp30) REVERT: E 62 ARG cc_start: 0.8385 (ttt90) cc_final: 0.8130 (ttt90) REVERT: F 50 GLU cc_start: 0.8009 (pt0) cc_final: 0.7306 (tm-30) REVERT: G 14 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7599 (mm-30) REVERT: G 20 ASP cc_start: 0.8130 (t70) cc_final: 0.7839 (t0) REVERT: G 22 TYR cc_start: 0.9082 (t80) cc_final: 0.8684 (t80) REVERT: K 58 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7815 (mmmm) REVERT: K 61 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: L 69 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7913 (tm-30) REVERT: L 76 GLU cc_start: 0.7813 (pp20) cc_final: 0.7584 (pp20) REVERT: N 20 ASP cc_start: 0.7988 (t0) cc_final: 0.7743 (t0) REVERT: O 5 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7989 (tpp-160) outliers start: 60 outliers final: 44 residues processed: 467 average time/residue: 0.3246 time to fit residues: 205.8040 Evaluate side-chains 457 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 410 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR 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 66 ARG 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 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 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 61 GLN 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 28 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 37 HIS 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 149 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 51 HIS F 61 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 37 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** O 37 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.119282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094094 restraints weight = 28924.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092932 restraints weight = 20180.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093870 restraints weight = 20579.447| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12677 Z= 0.169 Angle : 0.814 12.569 17060 Z= 0.412 Chirality : 0.045 0.277 1873 Planarity : 0.004 0.042 2183 Dihedral : 8.919 153.617 1738 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.26 % Allowed : 25.49 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1531 helix: 1.59 (0.16), residues: 1038 sheet: -1.09 (0.52), residues: 93 loop : -1.69 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 244 HIS 0.014 0.001 HIS E 51 PHE 0.024 0.001 PHE A 81 TYR 0.028 0.001 TYR I 58 ARG 0.008 0.001 ARG H 31 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 876) hydrogen bonds : angle 4.40356 ( 2592) SS BOND : bond 0.00556 ( 26) SS BOND : angle 2.76692 ( 52) covalent geometry : bond 0.00395 (12651) covalent geometry : angle 0.80076 (17008) *********************** 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 515 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 445 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7691 (mttp) REVERT: B 241 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8305 (mp) REVERT: C 199 VAL cc_start: 0.9054 (OUTLIER) cc_final: 0.8846 (t) REVERT: D 23 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9079 (mttt) REVERT: D 26 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 39 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7914 (tpt90) REVERT: E 50 GLU cc_start: 0.8518 (tp30) cc_final: 0.8208 (tp30) REVERT: E 62 ARG cc_start: 0.8256 (ttt90) cc_final: 0.8051 (ttt90) REVERT: F 62 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.7854 (ttm170) REVERT: G 17 MET cc_start: 0.8263 (ppp) cc_final: 0.7350 (ppp) REVERT: G 20 ASP cc_start: 0.8078 (t70) cc_final: 0.7838 (t0) REVERT: H 68 LYS cc_start: 0.8862 (tppt) cc_final: 0.8657 (tppt) REVERT: I 54 CYS cc_start: 0.3455 (m) cc_final: 0.2787 (m) REVERT: I 64 ARG cc_start: 0.8171 (ptm-80) cc_final: 0.7594 (ptm-80) REVERT: I 65 MET cc_start: 0.7789 (mmp) cc_final: 0.7370 (mmp) REVERT: J 10 GLN cc_start: 0.8488 (pt0) cc_final: 0.8225 (pt0) REVERT: K 58 LYS cc_start: 0.8239 (mmmm) cc_final: 0.7859 (mmtp) REVERT: K 61 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: L 69 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7908 (tm-30) REVERT: L 76 GLU cc_start: 0.7858 (pp20) cc_final: 0.7610 (pp20) REVERT: O 5 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7991 (tpp-160) REVERT: O 59 LEU cc_start: 0.8718 (mt) cc_final: 0.8373 (mt) outliers start: 70 outliers final: 54 residues processed: 477 average time/residue: 0.3074 time to fit residues: 196.2023 Evaluate side-chains 464 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 407 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 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 186 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 57 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 F residue 66 ARG 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 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 34 VAL Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 31 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 61 GLN 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 28 CYS 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 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 42 GLU 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 0 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 54 GLN L 68 GLN ** M 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.120083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.095032 restraints weight = 29273.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093544 restraints weight = 19357.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.094348 restraints weight = 21041.338| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12677 Z= 0.166 Angle : 0.851 13.124 17060 Z= 0.431 Chirality : 0.046 0.244 1873 Planarity : 0.004 0.044 2183 Dihedral : 8.809 153.956 1738 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.34 % Allowed : 27.29 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1531 helix: 1.45 (0.16), residues: 1054 sheet: -1.08 (0.52), residues: 94 loop : -1.58 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 244 HIS 0.013 0.001 HIS E 51 PHE 0.029 0.001 PHE A 81 TYR 0.023 0.001 TYR H 22 ARG 0.010 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 876) hydrogen bonds : angle 4.45822 ( 2592) SS BOND : bond 0.00572 ( 26) SS BOND : angle 2.70368 ( 52) covalent geometry : bond 0.00379 (12651) covalent geometry : angle 0.83921 (17008) *********************** 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 519 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 448 time to evaluate : 1.662 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 72 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7693 (mttp) REVERT: B 107 LYS cc_start: 0.8043 (mttm) cc_final: 0.7665 (mttm) REVERT: B 241 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8462 (mp) REVERT: D 23 LYS cc_start: 0.9387 (ttmt) cc_final: 0.9153 (mttt) REVERT: D 39 ARG cc_start: 0.8411 (ttp80) cc_final: 0.7975 (tpt90) REVERT: D 45 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8391 (mp0) REVERT: E 27 THR cc_start: 0.9271 (p) cc_final: 0.9055 (t) REVERT: E 54 GLN cc_start: 0.7776 (pt0) cc_final: 0.7402 (pt0) REVERT: F 62 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.7944 (ttm170) REVERT: G 14 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7921 (mm-30) REVERT: G 20 ASP cc_start: 0.7946 (t70) cc_final: 0.7685 (t0) REVERT: G 22 TYR cc_start: 0.9007 (t80) cc_final: 0.8645 (t80) REVERT: I 64 ARG cc_start: 0.8267 (ptm-80) cc_final: 0.7995 (ptm-80) REVERT: I 65 MET cc_start: 0.7793 (mmp) cc_final: 0.7490 (mmt) REVERT: K 58 LYS cc_start: 0.8287 (mmmm) cc_final: 0.7937 (mmtp) REVERT: K 61 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: L 69 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7969 (tm-30) REVERT: M 14 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7791 (tm-30) REVERT: N 63 GLU cc_start: 0.7061 (tt0) cc_final: 0.6845 (tt0) REVERT: O 59 LEU cc_start: 0.8611 (mt) cc_final: 0.8209 (mt) outliers start: 71 outliers final: 52 residues processed: 479 average time/residue: 0.3526 time to fit residues: 231.9090 Evaluate side-chains 470 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 416 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 226 TYR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 217 TYR 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 F residue 66 ARG 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 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 61 GLN 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 23 LYS Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 42 GLU 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 84 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 D 54 GLN E 51 HIS ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 68 GLN O 8 GLN ** O 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.115702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.090250 restraints weight = 29250.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.089013 restraints weight = 22498.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090029 restraints weight = 23378.765| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 12677 Z= 0.271 Angle : 0.918 13.856 17060 Z= 0.473 Chirality : 0.051 0.279 1873 Planarity : 0.005 0.043 2183 Dihedral : 9.043 145.655 1738 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.34 % Allowed : 27.29 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1531 helix: 1.21 (0.16), residues: 1052 sheet: -1.23 (0.53), residues: 92 loop : -1.52 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 178 HIS 0.016 0.002 HIS E 51 PHE 0.030 0.002 PHE A 81 TYR 0.026 0.002 TYR I 58 ARG 0.009 0.001 ARG H 31 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 876) hydrogen bonds : angle 4.69611 ( 2592) SS BOND : bond 0.00764 ( 26) SS BOND : angle 3.12116 ( 52) covalent geometry : bond 0.00642 (12651) covalent geometry : angle 0.90284 (17008) *********************** 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 490 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 419 time to evaluate : 1.941 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: A 72 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7921 (mttp) REVERT: B 241 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8369 (mp) REVERT: D 23 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9164 (mttt) REVERT: D 61 GLN cc_start: 0.8439 (mt0) cc_final: 0.7963 (mp10) REVERT: E 27 THR cc_start: 0.9280 (p) cc_final: 0.9039 (t) REVERT: F 62 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.7047 (ttm170) REVERT: F 66 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7501 (mpp-170) REVERT: I 64 ARG cc_start: 0.8333 (ptm-80) cc_final: 0.7776 (ptm-80) REVERT: I 65 MET cc_start: 0.7906 (mmp) cc_final: 0.7400 (mmt) outliers start: 71 outliers final: 53 residues processed: 463 average time/residue: 0.2927 time to fit residues: 185.4292 Evaluate side-chains 450 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 395 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain B residue 136 LEU 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 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 198 VAL 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 59 MET Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain G residue 72 LEU 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 34 VAL Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 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 23 LYS Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 42 GLU 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 46 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 95 optimal weight: 0.0470 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 0.0270 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 229 GLN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 GLN L 73 GLN ** O 30 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.119419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094157 restraints weight = 29124.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.092576 restraints weight = 20091.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093752 restraints weight = 20833.922| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12677 Z= 0.177 Angle : 0.951 14.322 17060 Z= 0.480 Chirality : 0.049 0.286 1873 Planarity : 0.005 0.047 2183 Dihedral : 8.865 142.178 1738 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.98 % Allowed : 29.40 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1531 helix: 1.33 (0.16), residues: 1047 sheet: -1.11 (0.53), residues: 91 loop : -1.43 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 244 HIS 0.019 0.001 HIS E 51 PHE 0.028 0.001 PHE A 81 TYR 0.025 0.001 TYR I 58 ARG 0.011 0.001 ARG N 64 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 876) hydrogen bonds : angle 4.64303 ( 2592) SS BOND : bond 0.00599 ( 26) SS BOND : angle 2.88320 ( 52) covalent geometry : bond 0.00400 (12651) covalent geometry : angle 0.93945 (17008) ********************** 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: 53 poor density : 434 time to evaluate : 1.517 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: A 72 LYS cc_start: 0.8158 (mtpt) cc_final: 0.7849 (mttp) REVERT: B 241 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8330 (mp) REVERT: C 198 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8172 (t) REVERT: D 23 LYS cc_start: 0.9425 (ttmt) cc_final: 0.9196 (mttt) REVERT: D 39 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7899 (tpt90) REVERT: D 45 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8377 (mp0) REVERT: E 27 THR cc_start: 0.9244 (p) cc_final: 0.9019 (t) REVERT: F 62 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.7990 (ttm170) REVERT: I 64 ARG cc_start: 0.8333 (ptm-80) cc_final: 0.7693 (ptm-80) REVERT: I 65 MET cc_start: 0.7942 (mmp) cc_final: 0.7357 (mmt) REVERT: J 23 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8282 (mtm110) REVERT: J 64 MET cc_start: 0.7822 (tpt) cc_final: 0.7609 (tpt) REVERT: K 34 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8580 (mmtm) REVERT: L 69 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8045 (tm-30) REVERT: O 59 LEU cc_start: 0.8547 (mt) cc_final: 0.8200 (mt) REVERT: O 63 GLU cc_start: 0.7446 (mp0) cc_final: 0.7184 (mp0) outliers start: 53 outliers final: 40 residues processed: 461 average time/residue: 0.2889 time to fit residues: 180.8882 Evaluate side-chains 454 residues out of total 1366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 412 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 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 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 186 ASP Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 198 VAL 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 F residue 66 ARG 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 72 LEU Chi-restraints excluded: chain K residue 61 GLN 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 23 LYS Chi-restraints excluded: chain L residue 48 CYS Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 68 GLN Chi-restraints excluded: chain L residue 73 GLN Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain M residue 31 ARG Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 7 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 68 GLN O 8 GLN ** O 30 HIS ** 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 = 0.3828 r_free = 0.3828 target = 0.118034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093319 restraints weight = 29560.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091524 restraints weight = 21007.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092603 restraints weight = 21346.042| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 12677 Z= 0.196 Angle : 0.974 14.841 17060 Z= 0.492 Chirality : 0.051 0.323 1873 Planarity : 0.005 0.045 2183 Dihedral : 8.867 142.029 1738 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.06 % Allowed : 30.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.22), residues: 1531 helix: 1.24 (0.16), residues: 1055 sheet: -0.92 (0.51), residues: 103 loop : -1.38 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 244 HIS 0.020 0.001 HIS E 51 PHE 0.029 0.002 PHE A 81 TYR 0.026 0.002 TYR J 67 ARG 0.008 0.001 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 876) hydrogen bonds : angle 4.73781 ( 2592) SS BOND : bond 0.00622 ( 26) SS BOND : angle 2.69425 ( 52) covalent geometry : bond 0.00460 (12651) covalent geometry : angle 0.96446 (17008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5277.89 seconds wall clock time: 93 minutes 58.12 seconds (5638.12 seconds total)