Starting phenix.real_space_refine on Thu Sep 26 00:26:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/09_2024/8gp3_34188.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/09_2024/8gp3_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/09_2024/8gp3_34188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/09_2024/8gp3_34188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/09_2024/8gp3_34188.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/09_2024/8gp3_34188.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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, 'HIS:plan': 1, 'ASP:plan': 3} 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, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 9.01, per 1000 atoms: 0.78 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: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.86 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: 3.87 Time building geometry restraints manager: 3.15 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: 7.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 30.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- 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 11760 Z= 0.258 Angle : 0.654 11.832 16043 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (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 TRP 0.010 0.001 TRP M 36 HIS 0.002 0.001 HIS A 210 PHE 0.020 0.001 PHE I 105 TYR 0.021 0.001 TYR L 50 ARG 0.003 0.000 ARG B 307 *********************** 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 fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.323 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: 0.7279 (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: 0.1896 time to fit residues: 21.8275 Evaluate side-chains 51 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 20.0000 chunk 112 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11760 Z= 0.204 Angle : 0.571 9.556 16043 Z= 0.289 Chirality : 0.042 0.135 1832 Planarity : 0.004 0.035 2055 Dihedral : 7.390 81.453 1670 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1480 helix: 0.66 (0.71), residues: 46 sheet: 0.45 (0.19), residues: 664 loop : -0.17 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 113 HIS 0.004 0.001 HIS I 38 PHE 0.015 0.001 PHE M 99 TYR 0.016 0.001 TYR L 50 ARG 0.003 0.000 ARG H 90 *********************** 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 68 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9610 (mmmt) cc_final: 0.9359 (mmmt) REVERT: B 249 TYR cc_start: 0.8725 (p90) cc_final: 0.8276 (p90) REVERT: H 80 ASN cc_start: 0.8845 (m-40) cc_final: 0.8506 (m-40) REVERT: H 93 ASP cc_start: 0.8141 (m-30) cc_final: 0.7586 (m-30) REVERT: I 93 ASP cc_start: 0.8087 (m-30) cc_final: 0.7531 (m-30) REVERT: M 3 ILE cc_start: 0.8304 (mm) cc_final: 0.7578 (mm) REVERT: M 5 MET cc_start: 0.8660 (mpp) cc_final: 0.8138 (tmm) REVERT: M 166 GLU cc_start: 0.9745 (tp30) cc_final: 0.9446 (tp30) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1889 time to fit residues: 21.1704 Evaluate side-chains 45 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 45 optimal weight: 0.0870 chunk 108 optimal weight: 0.0370 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 HIS H 85 GLN I 85 GLN L 38 GLN M 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11760 Z= 0.133 Angle : 0.541 10.155 16043 Z= 0.263 Chirality : 0.042 0.138 1832 Planarity : 0.004 0.062 2055 Dihedral : 7.117 79.426 1670 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1480 helix: 0.63 (0.69), residues: 46 sheet: 0.59 (0.20), residues: 660 loop : -0.12 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 36 HIS 0.002 0.000 HIS B 210 PHE 0.011 0.001 PHE I 105 TYR 0.017 0.001 TYR M 50 ARG 0.004 0.000 ARG H 101 *********************** 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 76 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9606 (mmmt) cc_final: 0.9342 (mmmt) REVERT: A 249 TYR cc_start: 0.8729 (p90) cc_final: 0.8465 (p90) REVERT: B 249 TYR cc_start: 0.8653 (p90) cc_final: 0.8211 (p90) REVERT: H 86 MET cc_start: 0.8827 (pmm) cc_final: 0.7798 (pmm) REVERT: H 93 ASP cc_start: 0.8178 (m-30) cc_final: 0.7653 (m-30) REVERT: I 86 MET cc_start: 0.8854 (pmm) cc_final: 0.7832 (pmm) REVERT: I 93 ASP cc_start: 0.8141 (m-30) cc_final: 0.7627 (m-30) REVERT: M 3 ILE cc_start: 0.8208 (mm) cc_final: 0.7555 (mm) REVERT: M 5 MET cc_start: 0.8574 (mpp) cc_final: 0.7770 (tmm) REVERT: M 50 TYR cc_start: 0.9643 (p90) cc_final: 0.9424 (p90) REVERT: M 166 GLU cc_start: 0.9731 (tp30) cc_final: 0.9413 (tp30) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.2049 time to fit residues: 24.4628 Evaluate side-chains 46 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 14 optimal weight: 0.0370 chunk 64 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 0.0010 chunk 38 optimal weight: 6.9990 overall best weight: 2.4070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11760 Z= 0.282 Angle : 0.624 10.973 16043 Z= 0.309 Chirality : 0.042 0.189 1832 Planarity : 0.004 0.039 2055 Dihedral : 7.417 79.768 1670 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1480 helix: 0.56 (0.68), residues: 46 sheet: 0.31 (0.20), residues: 640 loop : -0.33 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 36 HIS 0.007 0.002 HIS A 210 PHE 0.015 0.002 PHE B 27 TYR 0.016 0.002 TYR A 321 ARG 0.004 0.001 ARG B 307 *********************** 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 fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.363 Fit side-chains REVERT: H 86 MET cc_start: 0.8486 (pmm) cc_final: 0.8202 (pmm) REVERT: I 86 MET cc_start: 0.8527 (pmm) cc_final: 0.8235 (pmm) REVERT: L 3 ILE cc_start: 0.9287 (mt) cc_final: 0.8876 (mt) REVERT: L 5 MET cc_start: 0.8934 (mpp) cc_final: 0.8398 (tmm) REVERT: L 24 CYS cc_start: 0.5841 (t) cc_final: 0.5477 (p) REVERT: M 50 TYR cc_start: 0.9620 (p90) cc_final: 0.9306 (p90) REVERT: M 166 GLU cc_start: 0.9760 (tp30) cc_final: 0.9492 (tp30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1995 time to fit residues: 17.9417 Evaluate side-chains 37 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 11760 Z= 0.483 Angle : 0.841 16.180 16043 Z= 0.418 Chirality : 0.048 0.175 1832 Planarity : 0.006 0.054 2055 Dihedral : 8.364 81.283 1670 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.21), residues: 1480 helix: -0.10 (0.64), residues: 50 sheet: -0.34 (0.21), residues: 584 loop : -0.88 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP H 106 HIS 0.016 0.003 HIS A 210 PHE 0.026 0.003 PHE M 99 TYR 0.025 0.003 TYR A 321 ARG 0.009 0.001 ARG I 103 *********************** 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 42 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: M 50 TYR cc_start: 0.9556 (p90) cc_final: 0.9040 (p90) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1728 time to fit residues: 13.2667 Evaluate side-chains 34 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11760 Z= 0.206 Angle : 0.626 20.295 16043 Z= 0.299 Chirality : 0.044 0.192 1832 Planarity : 0.004 0.039 2055 Dihedral : 7.708 79.551 1670 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.12 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.21), residues: 1480 helix: 0.15 (0.62), residues: 50 sheet: -0.04 (0.21), residues: 596 loop : -0.70 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 36 HIS 0.004 0.001 HIS B 353 PHE 0.015 0.001 PHE H 105 TYR 0.013 0.001 TYR M 88 ARG 0.003 0.000 ARG H 103 *********************** 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 48 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.8675 (m) cc_final: 0.8450 (p) REVERT: M 50 TYR cc_start: 0.9544 (p90) cc_final: 0.9211 (p90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2024 time to fit residues: 16.2316 Evaluate side-chains 37 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 88 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11760 Z= 0.279 Angle : 0.662 21.318 16043 Z= 0.317 Chirality : 0.044 0.175 1832 Planarity : 0.004 0.041 2055 Dihedral : 7.779 79.689 1670 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1480 helix: 0.13 (0.63), residues: 50 sheet: -0.22 (0.21), residues: 580 loop : -0.67 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 36 HIS 0.010 0.002 HIS I 38 PHE 0.015 0.002 PHE M 99 TYR 0.023 0.002 TYR L 50 ARG 0.004 0.001 ARG I 103 *********************** 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 45 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.8797 (m) cc_final: 0.8517 (p) REVERT: M 50 TYR cc_start: 0.9520 (p90) cc_final: 0.9013 (p90) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2174 time to fit residues: 16.1078 Evaluate side-chains 36 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 90 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 chunk 129 optimal weight: 10.0000 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11760 Z= 0.148 Angle : 0.602 21.289 16043 Z= 0.278 Chirality : 0.044 0.182 1832 Planarity : 0.004 0.042 2055 Dihedral : 7.225 78.736 1670 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1480 helix: 0.33 (0.63), residues: 50 sheet: 0.16 (0.21), residues: 594 loop : -0.55 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 39 HIS 0.003 0.001 HIS A 210 PHE 0.011 0.001 PHE L 99 TYR 0.011 0.001 TYR A 249 ARG 0.002 0.000 ARG H 101 *********************** 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 51 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.8695 (m) cc_final: 0.8482 (p) REVERT: B 249 TYR cc_start: 0.8496 (p90) cc_final: 0.8232 (p90) REVERT: L 55 LEU cc_start: 0.9510 (pp) cc_final: 0.9299 (pp) REVERT: M 5 MET cc_start: 0.8234 (mpp) cc_final: 0.8027 (mpp) REVERT: M 50 TYR cc_start: 0.9530 (p90) cc_final: 0.9277 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2230 time to fit residues: 18.0067 Evaluate side-chains 37 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.0070 chunk 124 optimal weight: 9.9990 chunk 132 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 overall best weight: 1.6402 ------------------------------------------------------------------------------- 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** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11760 Z= 0.212 Angle : 0.616 19.627 16043 Z= 0.291 Chirality : 0.043 0.167 1832 Planarity : 0.004 0.040 2055 Dihedral : 7.300 79.107 1670 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.99 % Favored : 95.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1480 helix: 0.43 (0.63), residues: 50 sheet: 0.18 (0.21), residues: 608 loop : -0.59 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 39 HIS 0.008 0.001 HIS A 210 PHE 0.020 0.001 PHE H 105 TYR 0.025 0.002 TYR L 50 ARG 0.003 0.000 ARG L 25 *********************** 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 46 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.8758 (m) cc_final: 0.8521 (p) REVERT: L 55 LEU cc_start: 0.9505 (pp) cc_final: 0.9272 (pp) REVERT: M 49 ILE cc_start: 0.9483 (mp) cc_final: 0.9148 (tt) REVERT: M 50 TYR cc_start: 0.9504 (p90) cc_final: 0.9245 (p90) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2278 time to fit residues: 16.6356 Evaluate side-chains 39 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.0000 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 0.0270 chunk 12 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.0670 chunk 125 optimal weight: 1.9990 overall best weight: 0.1758 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11760 Z= 0.148 Angle : 0.609 18.696 16043 Z= 0.282 Chirality : 0.044 0.193 1832 Planarity : 0.004 0.043 2055 Dihedral : 6.863 78.842 1670 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.38 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1480 helix: 0.52 (0.65), residues: 50 sheet: 0.57 (0.21), residues: 602 loop : -0.55 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 106 HIS 0.003 0.001 HIS A 210 PHE 0.009 0.001 PHE L 99 TYR 0.019 0.001 TYR A 249 ARG 0.003 0.000 ARG H 22 ********************** 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 55 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.378 Fit side-chains revert: symmetry clash REVERT: A 249 TYR cc_start: 0.8892 (p90) cc_final: 0.8144 (p90) REVERT: B 249 TYR cc_start: 0.8409 (p90) cc_final: 0.8207 (p90) REVERT: L 55 LEU cc_start: 0.9502 (pp) cc_final: 0.9283 (pp) REVERT: M 49 ILE cc_start: 0.9484 (mp) cc_final: 0.9232 (tt) REVERT: M 50 TYR cc_start: 0.9553 (p90) cc_final: 0.9307 (p90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2041 time to fit residues: 18.2071 Evaluate side-chains 37 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 0.0000 overall best weight: 2.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** 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 = 0.3021 r_free = 0.3021 target = 0.041848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.029312 restraints weight = 105180.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.030375 restraints weight = 66577.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.031130 restraints weight = 49215.682| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11760 Z= 0.271 Angle : 0.657 18.199 16043 Z= 0.315 Chirality : 0.043 0.161 1832 Planarity : 0.005 0.042 2055 Dihedral : 7.305 79.265 1670 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1480 helix: 0.57 (0.62), residues: 50 sheet: 0.27 (0.21), residues: 590 loop : -0.56 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 106 HIS 0.010 0.002 HIS I 38 PHE 0.018 0.002 PHE L 99 TYR 0.030 0.002 TYR L 50 ARG 0.003 0.001 ARG L 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.14 seconds wall clock time: 41 minutes 32.84 seconds (2492.84 seconds total)