Starting phenix.real_space_refine on Sat Aug 23 11:00:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gp3_34188/08_2025/8gp3_34188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gp3_34188/08_2025/8gp3_34188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gp3_34188/08_2025/8gp3_34188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gp3_34188/08_2025/8gp3_34188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gp3_34188/08_2025/8gp3_34188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gp3_34188/08_2025/8gp3_34188.map" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 10 5.49 5 S 38 5.16 5 C 7275 2.51 5 N 1938 2.21 5 O 2233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11494 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2797 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 62 Chain: "V" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 89 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2805 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 52 Chain: "U" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 89 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1363 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 3.42, per 1000 atoms: 0.30 Number of scatterers: 11494 At special positions: 0 Unit cell: (107.116, 197.55, 99.214, 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 38 16.00 P 10 15.00 O 2233 8.00 N 1938 7.00 C 7275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 667.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 30 sheets defined 6.0% alpha, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.614A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.024A pdb=" N ASN A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.644A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.013A pdb=" N ARG B 282 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.185A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.855A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 4.261A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.163A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 129 removed outlier: 3.875A pdb=" N LYS M 127 " --> pdb=" O ASP M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 190 removed outlier: 4.258A pdb=" N HIS M 190 " --> pdb=" O ASP M 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 removed outlier: 3.520A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.831A pdb=" N VAL A 171 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 168 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY A 141 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 145 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.831A pdb=" N VAL A 171 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 168 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.562A pdb=" N TYR A 272 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.526A pdb=" N VAL A 343 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 349 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 249 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.703A pdb=" N GLU U 345 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.843A pdb=" N VAL B 171 " --> pdb=" O PHE B 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 85 removed outlier: 6.544A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 62 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 141 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 85 removed outlier: 6.544A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 62 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 141 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.555A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.533A pdb=" N VAL B 343 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 322 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR B 249 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 241 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.920A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 14 through 15 removed outlier: 8.875A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.629A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.586A pdb=" N LEU H 134 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.586A pdb=" N LEU H 134 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.581A pdb=" N VAL H 208 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.914A pdb=" N LEU I 21 " --> pdb=" O MET I 86 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET I 86 " --> pdb=" O LEU I 21 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU I 23 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 14 through 15 removed outlier: 8.840A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR I 62 " --> pdb=" O SER I 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 14 through 15 removed outlier: 3.739A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 130 through 134 removed outlier: 3.584A pdb=" N LEU I 134 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR I 186 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 130 through 134 removed outlier: 3.584A pdb=" N LEU I 134 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR I 186 " --> pdb=" O ASP I 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 161 through 164 removed outlier: 3.576A pdb=" N VAL I 208 " --> pdb=" O VAL I 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AC7, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.614A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.767A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 7 through 8 Processing sheet with id=AD1, first strand: chain 'M' and resid 11 through 14 removed outlier: 3.685A pdb=" N LEU M 12 " --> pdb=" O LYS M 104 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU M 106 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 49 through 50 Processing sheet with id=AD3, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.770A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3469 1.33 - 1.45: 1783 1.45 - 1.57: 6426 1.57 - 1.69: 34 1.69 - 1.81: 48 Bond restraints: 11760 Sorted by residual: bond pdb=" O3P SEP U 346 " pdb=" P SEP U 346 " ideal model delta sigma weight residual 1.610 1.505 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O2P SEP V 344 " pdb=" P SEP V 344 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O1P SEP U 346 " pdb=" P SEP U 346 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O3P SEP V 344 " pdb=" P SEP V 344 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O1P SEP V 344 " pdb=" P SEP V 344 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 11755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 15783 2.37 - 4.73: 241 4.73 - 7.10: 15 7.10 - 9.47: 2 9.47 - 11.83: 2 Bond angle restraints: 16043 Sorted by residual: angle pdb=" CA PHE B 75 " pdb=" C PHE B 75 " pdb=" N ARG B 76 " ideal model delta sigma weight residual 115.51 110.14 5.37 1.24e+00 6.50e-01 1.88e+01 angle pdb=" N VAL M 30 " pdb=" CA VAL M 30 " pdb=" C VAL M 30 " ideal model delta sigma weight residual 113.20 109.05 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" N VAL L 30 " pdb=" CA VAL L 30 " pdb=" C VAL L 30 " ideal model delta sigma weight residual 113.20 109.39 3.81 9.60e-01 1.09e+00 1.57e+01 angle pdb=" N GLY A 291 " pdb=" CA GLY A 291 " pdb=" C GLY A 291 " ideal model delta sigma weight residual 111.36 115.74 -4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" C CYS A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta sigma weight residual 122.59 116.75 5.84 1.57e+00 4.06e-01 1.39e+01 ... (remaining 16038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6446 17.30 - 34.61: 520 34.61 - 51.91: 71 51.91 - 69.21: 21 69.21 - 86.52: 15 Dihedral angle restraints: 7073 sinusoidal: 2629 harmonic: 4444 Sorted by residual: dihedral pdb=" CA HIS B 362 " pdb=" C HIS B 362 " pdb=" N ARG B 363 " pdb=" CA ARG B 363 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CA HIS A 362 " pdb=" C HIS A 362 " pdb=" N ARG A 363 " pdb=" CA ARG A 363 " ideal model delta harmonic sigma weight residual 180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" N SEP V 344 " pdb=" CA SEP V 344 " pdb=" CB SEP V 344 " pdb=" OG SEP V 344 " ideal model delta sinusoidal sigma weight residual 60.00 3.37 56.63 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 7070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1339 0.040 - 0.079: 298 0.079 - 0.119: 182 0.119 - 0.158: 9 0.158 - 0.198: 4 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CA ARG A 62 " pdb=" N ARG A 62 " pdb=" C ARG A 62 " pdb=" CB ARG A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA LEU B 68 " pdb=" N LEU B 68 " pdb=" C LEU B 68 " pdb=" CB LEU B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB THR A 6 " pdb=" CA THR A 6 " pdb=" OG1 THR A 6 " pdb=" CG2 THR A 6 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1829 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 61 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C PHE A 61 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE A 61 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG A 62 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 75 " 0.019 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C PHE B 75 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE B 75 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG B 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 67 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ASP B 67 " -0.067 2.00e-02 2.50e+03 pdb=" O ASP B 67 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 68 " 0.023 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 201 2.66 - 3.22: 10561 3.22 - 3.78: 17522 3.78 - 4.34: 22386 4.34 - 4.90: 36829 Nonbonded interactions: 87499 Sorted by model distance: nonbonded pdb=" NE2 GLN L 90 " pdb=" O GLN L 91 " model vdw 2.102 3.120 nonbonded pdb=" NE2 GLN M 90 " pdb=" O GLN M 91 " model vdw 2.201 3.120 nonbonded pdb=" O ILE B 31 " pdb=" NH2 ARG B 307 " model vdw 2.207 3.120 nonbonded pdb=" O3P SEP V 346 " pdb=" OG SER L 31 " model vdw 2.230 3.040 nonbonded pdb=" O ASP M 83 " pdb=" OH TYR M 87 " model vdw 2.237 3.040 ... (remaining 87494 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 'A' and (resid 6 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 133 or (resid 134 and (name N or na \ me CA or name C or name O or name CB )) or resid 135 through 368)) selection = (chain 'B' and (resid 6 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 190)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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=0.65 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: 12.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.450 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.004 0.105 11766 Z= 0.228 Angle : 0.654 11.832 16055 Z= 0.361 Chirality : 0.044 0.198 1832 Planarity : 0.004 0.041 2055 Dihedral : 13.226 86.515 4191 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1480 helix: 0.93 (0.75), residues: 46 sheet: 0.69 (0.21), residues: 582 loop : -0.35 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.021 0.001 TYR L 50 PHE 0.020 0.001 PHE I 105 TRP 0.010 0.001 TRP M 36 HIS 0.002 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00383 (11760) covalent geometry : angle 0.65414 (16043) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.42060 ( 12) hydrogen bonds : bond 0.29577 ( 397) hydrogen bonds : angle 9.64581 ( 1155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 30 PHE cc_start: 0.9010 (p90) cc_final: 0.8702 (p90) REVERT: H 80 ASN cc_start: 0.9041 (m-40) cc_final: 0.8733 (m-40) REVERT: H 93 ASP cc_start: 0.7814 (m-30) cc_final: 0.7278 (m-30) REVERT: I 30 PHE cc_start: 0.9095 (p90) cc_final: 0.8794 (p90) REVERT: I 93 ASP cc_start: 0.7775 (m-30) cc_final: 0.7237 (m-30) REVERT: M 50 TYR cc_start: 0.9744 (p90) cc_final: 0.9422 (p90) REVERT: M 166 GLU cc_start: 0.9744 (tp30) cc_final: 0.9433 (tp30) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0915 time to fit residues: 10.4039 Evaluate side-chains 52 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 30 HIS ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 HIS M 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.041671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.029236 restraints weight = 108736.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.030275 restraints weight = 69675.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.031027 restraints weight = 51832.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.031568 restraints weight = 42040.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.031952 restraints weight = 36317.260| |-----------------------------------------------------------------------------| r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 11766 Z= 0.351 Angle : 0.822 10.203 16055 Z= 0.413 Chirality : 0.046 0.186 1832 Planarity : 0.006 0.042 2055 Dihedral : 8.327 81.822 1670 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.68 % Rotamer: Outliers : 0.25 % Allowed : 9.23 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.21), residues: 1480 helix: 0.19 (0.70), residues: 46 sheet: -0.08 (0.19), residues: 662 loop : -0.77 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 70 TYR 0.024 0.003 TYR H 97 PHE 0.028 0.003 PHE M 99 TRP 0.012 0.003 TRP M 36 HIS 0.016 0.003 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00716 (11760) covalent geometry : angle 0.82124 (16043) SS BOND : bond 0.00845 ( 6) SS BOND : angle 1.15192 ( 12) hydrogen bonds : bond 0.05021 ( 397) hydrogen bonds : angle 7.47329 ( 1155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9409 (mmmt) REVERT: B 229 LYS cc_start: 0.9640 (mmmt) cc_final: 0.9418 (mmmt) REVERT: I 105 PHE cc_start: 0.9384 (m-80) cc_final: 0.8814 (m-80) REVERT: L 24 CYS cc_start: 0.3723 (t) cc_final: 0.2165 (t) REVERT: L 50 TYR cc_start: 0.9699 (p90) cc_final: 0.9495 (p90) REVERT: M 5 MET cc_start: 0.8927 (mpp) cc_final: 0.8669 (mpp) REVERT: M 50 TYR cc_start: 0.9744 (p90) cc_final: 0.9355 (p90) REVERT: M 166 GLU cc_start: 0.9764 (tp30) cc_final: 0.9526 (tp30) outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 0.0794 time to fit residues: 7.7205 Evaluate side-chains 42 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 0.0170 chunk 130 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN I 85 GLN L 38 GLN M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.043792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.030649 restraints weight = 100708.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.031856 restraints weight = 61966.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.032718 restraints weight = 44974.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033332 restraints weight = 35917.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.033769 restraints weight = 30704.019| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11766 Z= 0.118 Angle : 0.579 13.785 16055 Z= 0.282 Chirality : 0.043 0.146 1832 Planarity : 0.005 0.061 2055 Dihedral : 7.701 79.845 1670 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.21), residues: 1480 helix: 0.43 (0.71), residues: 46 sheet: 0.12 (0.20), residues: 628 loop : -0.57 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 41 TYR 0.014 0.001 TYR A 249 PHE 0.020 0.001 PHE L 99 TRP 0.008 0.001 TRP L 36 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00248 (11760) covalent geometry : angle 0.57926 (16043) SS BOND : bond 0.00354 ( 6) SS BOND : angle 0.40997 ( 12) hydrogen bonds : bond 0.03591 ( 397) hydrogen bonds : angle 6.47935 ( 1155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.9003 (mpp) cc_final: 0.8788 (mpp) REVERT: B 249 TYR cc_start: 0.8680 (p90) cc_final: 0.8352 (p90) REVERT: H 80 ASN cc_start: 0.8650 (m-40) cc_final: 0.8325 (t0) REVERT: H 85 GLN cc_start: 0.8881 (tp-100) cc_final: 0.8313 (mp10) REVERT: H 86 MET cc_start: 0.9258 (pmm) cc_final: 0.8831 (pmm) REVERT: H 93 ASP cc_start: 0.8020 (m-30) cc_final: 0.7369 (m-30) REVERT: I 49 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8392 (tm-30) REVERT: I 85 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8359 (mp10) REVERT: I 86 MET cc_start: 0.9272 (pmm) cc_final: 0.8855 (pmm) REVERT: I 93 ASP cc_start: 0.8029 (m-30) cc_final: 0.7257 (m-30) REVERT: L 49 ILE cc_start: 0.9371 (mm) cc_final: 0.9016 (tt) REVERT: M 166 GLU cc_start: 0.9763 (tp30) cc_final: 0.9524 (tp30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0987 time to fit residues: 9.4348 Evaluate side-chains 50 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.0060 chunk 68 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 20 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.042823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.029914 restraints weight = 102967.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.031084 restraints weight = 63767.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.031893 restraints weight = 46426.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032447 restraints weight = 37328.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.032862 restraints weight = 32182.357| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11766 Z= 0.162 Angle : 0.588 15.536 16055 Z= 0.287 Chirality : 0.042 0.141 1832 Planarity : 0.004 0.044 2055 Dihedral : 7.667 80.111 1670 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1480 helix: 0.42 (0.66), residues: 46 sheet: 0.09 (0.20), residues: 626 loop : -0.59 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 41 TYR 0.012 0.001 TYR H 98 PHE 0.018 0.001 PHE L 99 TRP 0.007 0.001 TRP H 113 HIS 0.007 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00341 (11760) covalent geometry : angle 0.58797 (16043) SS BOND : bond 0.00451 ( 6) SS BOND : angle 0.68231 ( 12) hydrogen bonds : bond 0.03312 ( 397) hydrogen bonds : angle 6.36419 ( 1155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 MET cc_start: 0.8999 (mpp) cc_final: 0.8765 (mpp) REVERT: H 93 ASP cc_start: 0.7902 (m-30) cc_final: 0.7256 (m-30) REVERT: L 49 ILE cc_start: 0.9399 (mm) cc_final: 0.9072 (tt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0997 time to fit residues: 8.6773 Evaluate side-chains 40 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.041598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.029349 restraints weight = 109198.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.030407 restraints weight = 68756.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.031161 restraints weight = 50715.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031699 restraints weight = 41015.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.032064 restraints weight = 35447.266| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11766 Z= 0.242 Angle : 0.695 18.264 16055 Z= 0.339 Chirality : 0.044 0.157 1832 Planarity : 0.004 0.040 2055 Dihedral : 8.019 80.984 1670 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1480 helix: 0.35 (0.64), residues: 46 sheet: -0.08 (0.20), residues: 618 loop : -0.80 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 103 TYR 0.021 0.002 TYR A 321 PHE 0.021 0.002 PHE L 99 TRP 0.009 0.002 TRP H 39 HIS 0.010 0.002 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00503 (11760) covalent geometry : angle 0.69532 (16043) SS BOND : bond 0.00777 ( 6) SS BOND : angle 0.66449 ( 12) hydrogen bonds : bond 0.03740 ( 397) hydrogen bonds : angle 6.55547 ( 1155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.495 Fit side-chains REVERT: A 215 SER cc_start: 0.8728 (m) cc_final: 0.8463 (p) REVERT: B 215 SER cc_start: 0.8696 (m) cc_final: 0.8464 (p) REVERT: H 86 MET cc_start: 0.8966 (pmm) cc_final: 0.8511 (pmm) REVERT: H 93 ASP cc_start: 0.8043 (m-30) cc_final: 0.7337 (m-30) REVERT: I 86 MET cc_start: 0.8979 (pmm) cc_final: 0.8707 (pmm) REVERT: L 24 CYS cc_start: 0.3497 (t) cc_final: 0.3078 (t) REVERT: L 49 ILE cc_start: 0.9385 (mm) cc_final: 0.9077 (tt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0982 time to fit residues: 8.2665 Evaluate side-chains 41 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 134 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 4 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.042230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.029698 restraints weight = 106500.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.030825 restraints weight = 66497.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.031604 restraints weight = 48563.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.032161 restraints weight = 39162.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.032546 restraints weight = 33721.716| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11766 Z= 0.159 Angle : 0.618 19.263 16055 Z= 0.296 Chirality : 0.043 0.149 1832 Planarity : 0.004 0.039 2055 Dihedral : 7.766 79.598 1670 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.21), residues: 1480 helix: -0.06 (0.63), residues: 46 sheet: -0.06 (0.21), residues: 588 loop : -0.62 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 103 TYR 0.012 0.001 TYR M 88 PHE 0.018 0.001 PHE H 105 TRP 0.011 0.002 TRP H 39 HIS 0.006 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00335 (11760) covalent geometry : angle 0.61794 (16043) SS BOND : bond 0.00450 ( 6) SS BOND : angle 0.63372 ( 12) hydrogen bonds : bond 0.03176 ( 397) hydrogen bonds : angle 6.23794 ( 1155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.8767 (m) cc_final: 0.8546 (p) REVERT: B 192 MET cc_start: 0.8981 (mpp) cc_final: 0.8773 (mpp) REVERT: B 215 SER cc_start: 0.8771 (m) cc_final: 0.8549 (p) REVERT: H 85 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8335 (mp10) REVERT: H 86 MET cc_start: 0.8994 (pmm) cc_final: 0.7978 (pmm) REVERT: H 93 ASP cc_start: 0.7898 (m-30) cc_final: 0.7234 (m-30) REVERT: I 49 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8600 (tm-30) REVERT: I 85 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8339 (mp10) REVERT: I 86 MET cc_start: 0.8975 (pmm) cc_final: 0.8136 (pmm) REVERT: I 93 ASP cc_start: 0.8824 (t70) cc_final: 0.8432 (m-30) REVERT: L 24 CYS cc_start: 0.3904 (t) cc_final: 0.3452 (t) REVERT: L 49 ILE cc_start: 0.9427 (mm) cc_final: 0.9093 (tt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0970 time to fit residues: 8.6263 Evaluate side-chains 44 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.030312 restraints weight = 102415.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031476 restraints weight = 63679.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032276 restraints weight = 46427.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.032860 restraints weight = 37372.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.033272 restraints weight = 32080.921| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11766 Z= 0.112 Angle : 0.585 18.806 16055 Z= 0.277 Chirality : 0.043 0.143 1832 Planarity : 0.004 0.040 2055 Dihedral : 7.483 78.187 1670 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.22), residues: 1480 helix: -0.17 (0.65), residues: 46 sheet: 0.18 (0.21), residues: 584 loop : -0.59 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 103 TYR 0.016 0.001 TYR B 238 PHE 0.013 0.001 PHE H 105 TRP 0.011 0.001 TRP H 39 HIS 0.003 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00243 (11760) covalent geometry : angle 0.58479 (16043) SS BOND : bond 0.00437 ( 6) SS BOND : angle 0.49906 ( 12) hydrogen bonds : bond 0.02880 ( 397) hydrogen bonds : angle 5.88942 ( 1155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 249 TYR cc_start: 0.8499 (p90) cc_final: 0.8241 (p90) REVERT: H 80 ASN cc_start: 0.8667 (m-40) cc_final: 0.8460 (m-40) REVERT: H 85 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8320 (mp10) REVERT: H 86 MET cc_start: 0.8961 (pmm) cc_final: 0.7934 (pmm) REVERT: H 93 ASP cc_start: 0.7881 (m-30) cc_final: 0.7192 (m-30) REVERT: I 49 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8532 (tm-30) REVERT: I 86 MET cc_start: 0.8937 (pmm) cc_final: 0.7757 (pmm) REVERT: I 93 ASP cc_start: 0.8763 (t70) cc_final: 0.8510 (m-30) REVERT: L 24 CYS cc_start: 0.3726 (t) cc_final: 0.1870 (t) REVERT: L 49 ILE cc_start: 0.9425 (mm) cc_final: 0.9169 (tp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0838 time to fit residues: 7.6419 Evaluate side-chains 43 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 82 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 chunk 73 optimal weight: 0.0170 chunk 103 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.043778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.030771 restraints weight = 100580.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.031992 restraints weight = 61502.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.032840 restraints weight = 44401.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.033447 restraints weight = 35487.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.033874 restraints weight = 30272.069| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11766 Z= 0.093 Angle : 0.580 17.357 16055 Z= 0.271 Chirality : 0.043 0.140 1832 Planarity : 0.004 0.042 2055 Dihedral : 7.171 77.735 1670 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.22), residues: 1480 helix: -0.02 (0.68), residues: 46 sheet: 0.46 (0.22), residues: 588 loop : -0.56 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 103 TYR 0.011 0.001 TYR A 249 PHE 0.019 0.001 PHE I 105 TRP 0.011 0.001 TRP H 39 HIS 0.002 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00209 (11760) covalent geometry : angle 0.57993 (16043) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.54439 ( 12) hydrogen bonds : bond 0.02664 ( 397) hydrogen bonds : angle 5.49117 ( 1155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: B 249 TYR cc_start: 0.8421 (p90) cc_final: 0.8177 (p90) REVERT: H 80 ASN cc_start: 0.8547 (m-40) cc_final: 0.8338 (m-40) REVERT: H 85 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8300 (mp10) REVERT: H 86 MET cc_start: 0.8949 (pmm) cc_final: 0.7949 (pmm) REVERT: H 93 ASP cc_start: 0.7947 (m-30) cc_final: 0.7306 (m-30) REVERT: I 49 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8446 (tm-30) REVERT: I 86 MET cc_start: 0.8531 (pmm) cc_final: 0.8009 (pmm) REVERT: I 93 ASP cc_start: 0.8772 (t70) cc_final: 0.8530 (m-30) REVERT: I 105 PHE cc_start: 0.9389 (m-80) cc_final: 0.8905 (m-10) REVERT: L 49 ILE cc_start: 0.9391 (mm) cc_final: 0.9114 (tp) REVERT: M 55 LEU cc_start: 0.9471 (pp) cc_final: 0.9232 (pp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0901 time to fit residues: 8.8204 Evaluate side-chains 44 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 144 optimal weight: 0.0870 chunk 41 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 100 optimal weight: 0.0980 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.030091 restraints weight = 105205.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.031204 restraints weight = 65803.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.031989 restraints weight = 48251.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.032525 restraints weight = 38965.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.032921 restraints weight = 33636.589| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11766 Z= 0.153 Angle : 0.597 16.433 16055 Z= 0.285 Chirality : 0.042 0.146 1832 Planarity : 0.004 0.042 2055 Dihedral : 7.361 78.404 1670 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.22), residues: 1480 helix: 0.16 (0.66), residues: 46 sheet: 0.28 (0.21), residues: 606 loop : -0.58 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 22 TYR 0.024 0.002 TYR M 50 PHE 0.025 0.001 PHE I 105 TRP 0.010 0.002 TRP I 113 HIS 0.007 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00322 (11760) covalent geometry : angle 0.59702 (16043) SS BOND : bond 0.00501 ( 6) SS BOND : angle 0.47230 ( 12) hydrogen bonds : bond 0.02887 ( 397) hydrogen bonds : angle 5.66454 ( 1155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.441 Fit side-chains REVERT: H 80 ASN cc_start: 0.8637 (m-40) cc_final: 0.8437 (m-40) REVERT: H 86 MET cc_start: 0.9102 (pmm) cc_final: 0.8563 (pmm) REVERT: H 93 ASP cc_start: 0.7957 (m-30) cc_final: 0.7272 (m-30) REVERT: I 86 MET cc_start: 0.8570 (pmm) cc_final: 0.8227 (pmm) REVERT: I 93 ASP cc_start: 0.8798 (t70) cc_final: 0.8500 (m-30) REVERT: I 105 PHE cc_start: 0.9426 (m-80) cc_final: 0.8925 (m-10) REVERT: L 3 ILE cc_start: 0.9267 (mt) cc_final: 0.8745 (mt) REVERT: L 5 MET cc_start: 0.8944 (mpp) cc_final: 0.8344 (tmm) REVERT: L 24 CYS cc_start: 0.6498 (t) cc_final: 0.3650 (t) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1005 time to fit residues: 8.4416 Evaluate side-chains 38 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 110 optimal weight: 0.3980 chunk 124 optimal weight: 0.0870 chunk 139 optimal weight: 0.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.043726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.030734 restraints weight = 102448.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.031928 restraints weight = 62747.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.032767 restraints weight = 45470.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.033357 restraints weight = 36381.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.033762 restraints weight = 31196.411| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11766 Z= 0.096 Angle : 0.580 16.750 16055 Z= 0.273 Chirality : 0.043 0.142 1832 Planarity : 0.004 0.042 2055 Dihedral : 7.116 78.161 1670 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.84 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.22), residues: 1480 helix: 0.05 (0.71), residues: 46 sheet: 0.50 (0.21), residues: 608 loop : -0.57 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 101 TYR 0.012 0.001 TYR A 249 PHE 0.021 0.001 PHE I 105 TRP 0.017 0.001 TRP I 39 HIS 0.003 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00215 (11760) covalent geometry : angle 0.57981 (16043) SS BOND : bond 0.00394 ( 6) SS BOND : angle 0.47580 ( 12) hydrogen bonds : bond 0.02669 ( 397) hydrogen bonds : angle 5.46021 ( 1155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: B 249 TYR cc_start: 0.8427 (p90) cc_final: 0.8224 (p90) REVERT: H 86 MET cc_start: 0.8506 (pmm) cc_final: 0.7911 (pmm) REVERT: H 93 ASP cc_start: 0.7921 (m-30) cc_final: 0.7262 (m-30) REVERT: I 86 MET cc_start: 0.8466 (pmm) cc_final: 0.8177 (pmm) REVERT: I 93 ASP cc_start: 0.8829 (t70) cc_final: 0.8561 (m-30) REVERT: L 3 ILE cc_start: 0.9211 (mt) cc_final: 0.8747 (mt) REVERT: L 5 MET cc_start: 0.8822 (mpp) cc_final: 0.8190 (tmm) REVERT: L 24 CYS cc_start: 0.6102 (t) cc_final: 0.5177 (t) REVERT: M 55 LEU cc_start: 0.9452 (pp) cc_final: 0.9199 (pp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0869 time to fit residues: 7.6850 Evaluate side-chains 41 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 44 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.042332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029677 restraints weight = 105054.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030770 restraints weight = 65871.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031543 restraints weight = 48352.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.032095 restraints weight = 39161.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.032485 restraints weight = 33724.492| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11766 Z= 0.165 Angle : 0.606 15.823 16055 Z= 0.293 Chirality : 0.042 0.148 1832 Planarity : 0.004 0.041 2055 Dihedral : 7.348 78.814 1670 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.92 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.22), residues: 1480 helix: 0.10 (0.68), residues: 46 sheet: 0.25 (0.21), residues: 612 loop : -0.60 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 101 TYR 0.029 0.002 TYR L 50 PHE 0.025 0.001 PHE I 105 TRP 0.010 0.002 TRP I 113 HIS 0.008 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00345 (11760) covalent geometry : angle 0.60622 (16043) SS BOND : bond 0.00594 ( 6) SS BOND : angle 0.73351 ( 12) hydrogen bonds : bond 0.02966 ( 397) hydrogen bonds : angle 5.68790 ( 1155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.96 seconds wall clock time: 34 minutes 40.10 seconds (2080.10 seconds total)