Starting phenix.real_space_refine on Fri Sep 27 04:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/09_2024/6vx6_21431.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/09_2024/6vx6_21431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/09_2024/6vx6_21431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/09_2024/6vx6_21431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/09_2024/6vx6_21431.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vx6_21431/09_2024/6vx6_21431.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 95 5.16 5 Cl 1 4.86 5 C 9870 2.51 5 N 2485 2.21 5 O 2605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15061 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 3011 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 7.76, per 1000 atoms: 0.52 Number of scatterers: 15061 At special positions: 0 Unit cell: (97.94, 96.28, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 95 16.00 O 2605 8.00 N 2485 7.00 C 9870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 69.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'E' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA E 10 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU E 22 " --> pdb=" O LYS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 37 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.533A pdb=" N ARG E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.790A pdb=" N CYS E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 149 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU E 210 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY E 263 " --> pdb=" O PRO E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER E 318 " --> pdb=" O CYS E 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU A 22 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 37 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.789A pdb=" N CYS A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY A 263 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 4.346A pdb=" N SER A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA B 10 " --> pdb=" O ALA B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.726A pdb=" N LEU B 22 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 37 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 139 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.940A pdb=" N LYS B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.654A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.565A pdb=" N GLY B 263 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.968A pdb=" N ALA C 10 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU C 22 " --> pdb=" O LYS C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 52 removed outlier: 5.928A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 37 " --> pdb=" O TRP C 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.960A pdb=" N VAL C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.725A pdb=" N ARG C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.568A pdb=" N CYS C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY C 263 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 294 removed outlier: 3.839A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 removed outlier: 3.969A pdb=" N ALA D 10 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.725A pdb=" N LEU D 22 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 52 removed outlier: 5.927A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 37 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.532A pdb=" N ARG D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.959A pdb=" N VAL D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.791A pdb=" N CYS D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.726A pdb=" N ARG D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 164 through 173 removed outlier: 3.941A pdb=" N LYS D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.569A pdb=" N CYS D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.653A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.862A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.566A pdb=" N GLY D 263 " --> pdb=" O PRO D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 294 removed outlier: 3.838A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 removed outlier: 4.347A pdb=" N SER D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2250 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: 4.13 Time building geometry restraints manager: 4.06 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: 4103 1.33 - 1.45: 3153 1.45 - 1.57: 8069 1.57 - 1.69: 0 1.69 - 1.81: 145 Bond restraints: 15470 Sorted by residual: bond pdb=" N VAL A 183 " pdb=" CA VAL A 183 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.90e+00 bond pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.75e+00 bond pdb=" N VAL E 183 " pdb=" CA VAL E 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.58e+00 bond pdb=" N VAL C 183 " pdb=" CA VAL C 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.51e+00 bond pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.47e+00 ... (remaining 15465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 20235 1.91 - 3.83: 599 3.83 - 5.74: 117 5.74 - 7.65: 24 7.65 - 9.56: 5 Bond angle restraints: 20980 Sorted by residual: angle pdb=" N LEU B 88 " pdb=" CA LEU B 88 " pdb=" C LEU B 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU D 88 " pdb=" CA LEU D 88 " pdb=" C LEU D 88 " ideal model delta sigma weight residual 111.82 106.39 5.43 1.16e+00 7.43e-01 2.19e+01 angle pdb=" N LEU E 88 " pdb=" CA LEU E 88 " pdb=" C LEU E 88 " ideal model delta sigma weight residual 111.82 106.42 5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N LEU A 88 " pdb=" CA LEU A 88 " pdb=" C LEU A 88 " ideal model delta sigma weight residual 111.82 106.43 5.39 1.16e+00 7.43e-01 2.16e+01 angle pdb=" N LEU C 88 " pdb=" CA LEU C 88 " pdb=" C LEU C 88 " ideal model delta sigma weight residual 111.82 106.44 5.38 1.16e+00 7.43e-01 2.15e+01 ... (remaining 20975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 7840 15.45 - 30.91: 910 30.91 - 46.36: 155 46.36 - 61.82: 45 61.82 - 77.27: 25 Dihedral angle restraints: 8975 sinusoidal: 3575 harmonic: 5400 Sorted by residual: dihedral pdb=" C VAL A 183 " pdb=" N VAL A 183 " pdb=" CA VAL A 183 " pdb=" CB VAL A 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL D 183 " pdb=" N VAL D 183 " pdb=" CA VAL D 183 " pdb=" CB VAL D 183 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C VAL C 183 " pdb=" N VAL C 183 " pdb=" CA VAL C 183 " pdb=" CB VAL C 183 " ideal model delta harmonic sigma weight residual -122.00 -131.83 9.83 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1739 0.053 - 0.105: 419 0.105 - 0.158: 76 0.158 - 0.210: 26 0.210 - 0.263: 15 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO C 77 " pdb=" N PRO C 77 " pdb=" C PRO C 77 " pdb=" CB PRO C 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO D 77 " pdb=" N PRO D 77 " pdb=" C PRO D 77 " pdb=" CB PRO D 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA PRO E 77 " pdb=" N PRO E 77 " pdb=" C PRO E 77 " pdb=" CB PRO E 77 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2272 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 351 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C THR A 351 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 351 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA A 352 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C THR B 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 352 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 351 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C THR C 351 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 351 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 352 " -0.016 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4107 2.79 - 3.32: 12796 3.32 - 3.84: 25125 3.84 - 4.37: 32863 4.37 - 4.90: 53533 Nonbonded interactions: 128424 Sorted by model distance: nonbonded pdb=" O ASN C 296 " pdb="CA CA C 501 " model vdw 2.260 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 501 " model vdw 2.273 2.510 nonbonded pdb=" O ALA C 10 " pdb="CA CA D 501 " model vdw 2.277 2.510 nonbonded pdb=" O LEU A 75 " pdb=" OH TYR A 284 " model vdw 2.289 3.040 nonbonded pdb=" O LEU B 75 " pdb=" OH TYR B 284 " model vdw 2.289 3.040 ... (remaining 128419 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 2 through 367) selection = (chain 'B' and resid 2 through 367) selection = (chain 'C' and resid 2 through 367) selection = (chain 'D' and resid 2 through 367) selection = (chain 'E' and resid 2 through 367) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.340 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 32.760 Find NCS groups from input model: 0.830 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: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.005 0.045 15470 Z= 0.300 Angle : 0.819 9.563 20980 Z= 0.492 Chirality : 0.053 0.263 2275 Planarity : 0.004 0.040 2625 Dihedral : 14.085 77.272 5505 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.12), residues: 1820 helix: -4.58 (0.05), residues: 1055 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 93 HIS 0.002 0.000 HIS D 115 PHE 0.020 0.002 PHE D 282 TYR 0.031 0.002 TYR D 236 ARG 0.019 0.001 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 263 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 165 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7512 (mpt180) REVERT: A 175 ASN cc_start: 0.7994 (t0) cc_final: 0.7779 (m-40) REVERT: A 203 ASP cc_start: 0.7708 (m-30) cc_final: 0.7471 (m-30) REVERT: D 64 LYS cc_start: 0.7760 (mttm) cc_final: 0.7468 (mtpt) REVERT: D 68 TYR cc_start: 0.7975 (t80) cc_final: 0.7760 (t80) outliers start: 15 outliers final: 0 residues processed: 278 average time/residue: 1.5485 time to fit residues: 467.1895 Evaluate side-chains 162 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 293 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 GLN A 296 ASN A 361 GLN B 58 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 293 GLN D 361 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15470 Z= 0.241 Angle : 0.582 10.797 20980 Z= 0.301 Chirality : 0.039 0.129 2275 Planarity : 0.004 0.025 2625 Dihedral : 4.356 15.161 2055 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.82 % Allowed : 14.47 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.16), residues: 1820 helix: -2.03 (0.12), residues: 1090 sheet: None (None), residues: 0 loop : -1.66 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 182 HIS 0.002 0.001 HIS B 115 PHE 0.021 0.002 PHE B 283 TYR 0.019 0.002 TYR D 236 ARG 0.005 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.7033 (m-10) cc_final: 0.6805 (m-10) REVERT: A 203 ASP cc_start: 0.7753 (m-30) cc_final: 0.7463 (m-30) REVERT: A 334 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7907 (mmtp) REVERT: B 34 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7686 (mtt90) REVERT: B 64 LYS cc_start: 0.7585 (mttm) cc_final: 0.7221 (mtpt) outliers start: 29 outliers final: 8 residues processed: 217 average time/residue: 1.3466 time to fit residues: 320.9220 Evaluate side-chains 171 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15470 Z= 0.197 Angle : 0.514 10.745 20980 Z= 0.260 Chirality : 0.038 0.119 2275 Planarity : 0.003 0.023 2625 Dihedral : 4.025 15.426 2055 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.14 % Allowed : 15.85 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 1820 helix: -0.56 (0.14), residues: 1105 sheet: None (None), residues: 0 loop : -1.37 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.002 0.000 HIS D 91 PHE 0.021 0.001 PHE E 80 TYR 0.014 0.001 TYR D 236 ARG 0.004 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7712 (ttm170) REVERT: A 203 ASP cc_start: 0.7808 (m-30) cc_final: 0.7528 (m-30) REVERT: A 262 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7334 (mm110) REVERT: A 334 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.7968 (mmtp) REVERT: B 34 ARG cc_start: 0.7906 (ttm110) cc_final: 0.7603 (mtt90) REVERT: B 64 LYS cc_start: 0.7593 (mttm) cc_final: 0.7322 (mtpt) REVERT: B 163 MET cc_start: 0.9281 (ttm) cc_final: 0.9071 (ttp) REVERT: C 64 LYS cc_start: 0.7788 (mttm) cc_final: 0.7568 (mtpt) REVERT: C 165 ARG cc_start: 0.7642 (tpp-160) cc_final: 0.7303 (mpt180) REVERT: D 11 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8129 (ttpt) REVERT: D 168 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.8005 (ttm110) outliers start: 34 outliers final: 15 residues processed: 233 average time/residue: 1.4182 time to fit residues: 361.0446 Evaluate side-chains 196 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 328 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 ASN A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 ASN D 280 GLN D 361 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.177 Angle : 0.508 11.440 20980 Z= 0.251 Chirality : 0.038 0.118 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.870 15.314 2055 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.33 % Allowed : 16.23 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 1820 helix: 0.17 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -1.19 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.004 0.001 HIS A 91 PHE 0.019 0.001 PHE B 276 TYR 0.016 0.001 TYR D 68 ARG 0.005 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 71 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7575 (ptm-80) REVERT: E 168 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7688 (ttm170) REVERT: A 203 ASP cc_start: 0.7790 (m-30) cc_final: 0.7520 (m-30) REVERT: B 64 LYS cc_start: 0.7593 (mttm) cc_final: 0.7309 (mtpt) REVERT: B 163 MET cc_start: 0.9246 (ttm) cc_final: 0.9016 (ttp) REVERT: C 64 LYS cc_start: 0.7730 (mttm) cc_final: 0.7468 (mtpt) REVERT: C 165 ARG cc_start: 0.7656 (tpp-160) cc_final: 0.7286 (mpt180) REVERT: D 168 ARG cc_start: 0.8191 (ttp-110) cc_final: 0.7949 (ttm110) outliers start: 37 outliers final: 19 residues processed: 226 average time/residue: 1.3877 time to fit residues: 344.1165 Evaluate side-chains 202 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 chunk 148 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.186 Angle : 0.507 11.318 20980 Z= 0.254 Chirality : 0.039 0.155 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.806 15.560 2055 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.95 % Allowed : 17.04 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1820 helix: 0.63 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.003 0.001 HIS C 91 PHE 0.019 0.001 PHE B 80 TYR 0.018 0.001 TYR A 68 ARG 0.003 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7711 (ttm170) REVERT: E 361 GLN cc_start: 0.7657 (mt0) cc_final: 0.7321 (mm-40) REVERT: A 203 ASP cc_start: 0.7805 (m-30) cc_final: 0.7553 (m-30) REVERT: A 334 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8024 (mmtp) REVERT: B 64 LYS cc_start: 0.7481 (mttm) cc_final: 0.7256 (mtpt) REVERT: B 163 MET cc_start: 0.9243 (ttm) cc_final: 0.9024 (ttp) REVERT: C 64 LYS cc_start: 0.7647 (mttm) cc_final: 0.7417 (mtpt) REVERT: C 165 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7326 (mpt180) outliers start: 31 outliers final: 17 residues processed: 225 average time/residue: 1.3216 time to fit residues: 326.7325 Evaluate side-chains 201 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15470 Z= 0.162 Angle : 0.510 11.828 20980 Z= 0.250 Chirality : 0.038 0.143 2275 Planarity : 0.003 0.023 2625 Dihedral : 3.735 15.159 2055 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.70 % Allowed : 18.43 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.19), residues: 1820 helix: 0.94 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -0.86 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 PHE 0.018 0.001 PHE D 80 TYR 0.025 0.001 TYR D 68 ARG 0.003 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 168 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7675 (ttm170) REVERT: E 361 GLN cc_start: 0.7673 (mt0) cc_final: 0.7358 (mm-40) REVERT: A 203 ASP cc_start: 0.7812 (m-30) cc_final: 0.7560 (m-30) REVERT: B 163 MET cc_start: 0.9239 (ttm) cc_final: 0.9001 (ttp) REVERT: C 165 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.7347 (mpt180) outliers start: 27 outliers final: 16 residues processed: 224 average time/residue: 1.3385 time to fit residues: 329.7874 Evaluate side-chains 201 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 0.0270 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.190 Angle : 0.516 10.976 20980 Z= 0.256 Chirality : 0.038 0.138 2275 Planarity : 0.003 0.033 2625 Dihedral : 3.755 15.320 2055 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.82 % Allowed : 19.31 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.19), residues: 1820 helix: 0.97 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.92 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 PHE 0.015 0.001 PHE C 80 TYR 0.011 0.001 TYR C 236 ARG 0.008 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8805 (mp) REVERT: E 168 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7714 (ttm170) REVERT: E 175 ASN cc_start: 0.7876 (t0) cc_final: 0.7611 (m110) REVERT: E 361 GLN cc_start: 0.7746 (mt0) cc_final: 0.7418 (mm-40) REVERT: A 203 ASP cc_start: 0.7844 (m-30) cc_final: 0.7574 (m-30) REVERT: B 163 MET cc_start: 0.9230 (ttm) cc_final: 0.8985 (ttp) REVERT: C 165 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7361 (mpt180) outliers start: 29 outliers final: 17 residues processed: 216 average time/residue: 1.2667 time to fit residues: 302.2161 Evaluate side-chains 208 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 331 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15470 Z= 0.192 Angle : 0.531 12.171 20980 Z= 0.260 Chirality : 0.039 0.133 2275 Planarity : 0.003 0.024 2625 Dihedral : 3.751 14.650 2055 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.01 % Allowed : 19.50 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1820 helix: 1.07 (0.15), residues: 1175 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.002 0.000 HIS A 91 PHE 0.020 0.002 PHE C 276 TYR 0.025 0.001 TYR D 68 ARG 0.005 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8757 (mp) REVERT: E 168 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: E 175 ASN cc_start: 0.7876 (t0) cc_final: 0.7586 (m110) REVERT: E 361 GLN cc_start: 0.7739 (mt0) cc_final: 0.7421 (mm-40) REVERT: A 168 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7414 (ttm170) REVERT: A 203 ASP cc_start: 0.7850 (m-30) cc_final: 0.7580 (m-30) REVERT: B 163 MET cc_start: 0.9221 (ttm) cc_final: 0.8974 (ttp) REVERT: C 68 TYR cc_start: 0.7884 (t80) cc_final: 0.7548 (t80) REVERT: C 77 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8623 (Cg_endo) REVERT: C 165 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7387 (mpt180) REVERT: D 42 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8816 (mp) REVERT: D 107 MET cc_start: 0.8827 (ptt) cc_final: 0.8589 (ptt) outliers start: 32 outliers final: 16 residues processed: 225 average time/residue: 1.2640 time to fit residues: 313.4644 Evaluate side-chains 207 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain D residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 151 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15470 Z= 0.221 Angle : 0.541 11.566 20980 Z= 0.267 Chirality : 0.039 0.129 2275 Planarity : 0.003 0.057 2625 Dihedral : 3.807 14.960 2055 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.64 % Allowed : 19.50 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.20), residues: 1820 helix: 1.07 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.82 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.002 0.001 HIS D 91 PHE 0.017 0.001 PHE A 282 TYR 0.014 0.001 TYR C 236 ARG 0.008 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8748 (mp) REVERT: E 168 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7733 (ttm170) REVERT: E 175 ASN cc_start: 0.7934 (t0) cc_final: 0.7628 (m110) REVERT: E 361 GLN cc_start: 0.7725 (mt0) cc_final: 0.7407 (mm-40) REVERT: A 168 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: A 203 ASP cc_start: 0.7882 (m-30) cc_final: 0.7607 (m-30) REVERT: B 163 MET cc_start: 0.9227 (ttm) cc_final: 0.9019 (ttp) REVERT: C 71 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7647 (ptm-80) REVERT: C 77 PRO cc_start: 0.8868 (Cg_exo) cc_final: 0.8665 (Cg_endo) REVERT: C 165 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7372 (mpt180) REVERT: D 42 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8820 (mp) REVERT: D 107 MET cc_start: 0.8853 (ptt) cc_final: 0.8613 (ptt) outliers start: 26 outliers final: 16 residues processed: 211 average time/residue: 1.2788 time to fit residues: 297.0988 Evaluate side-chains 211 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 chunk 118 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 142 optimal weight: 0.0040 chunk 14 optimal weight: 0.1980 chunk 110 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN E 95 ASN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15470 Z= 0.127 Angle : 0.507 12.666 20980 Z= 0.248 Chirality : 0.037 0.130 2275 Planarity : 0.003 0.045 2625 Dihedral : 3.686 15.673 2055 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.51 % Allowed : 20.13 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1820 helix: 1.25 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.80 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.003 0.000 HIS A 91 PHE 0.019 0.001 PHE A 276 TYR 0.024 0.001 TYR D 68 ARG 0.007 0.000 ARG B 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 204 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 42 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8783 (mp) REVERT: E 168 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7676 (ttm170) REVERT: E 175 ASN cc_start: 0.7782 (t0) cc_final: 0.7542 (m110) REVERT: E 361 GLN cc_start: 0.7674 (mt0) cc_final: 0.7311 (mm-40) REVERT: A 168 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7330 (ttm170) REVERT: A 203 ASP cc_start: 0.7807 (m-30) cc_final: 0.7417 (m-30) REVERT: B 163 MET cc_start: 0.9201 (ttm) cc_final: 0.8941 (ttp) REVERT: C 71 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7625 (ptm-80) REVERT: C 77 PRO cc_start: 0.8833 (Cg_exo) cc_final: 0.8624 (Cg_endo) REVERT: C 165 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7313 (mpt180) REVERT: C 175 ASN cc_start: 0.7894 (t0) cc_final: 0.7635 (m110) REVERT: D 107 MET cc_start: 0.8823 (ptt) cc_final: 0.8620 (ptt) outliers start: 24 outliers final: 16 residues processed: 219 average time/residue: 1.3233 time to fit residues: 319.1960 Evaluate side-chains 212 residues out of total 1590 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 ARG Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 168 ARG Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 251 CYS Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 25 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 251 CYS Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 GLN ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 308 ASN B 361 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN C 361 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107786 restraints weight = 18817.783| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.95 r_work: 0.3220 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15470 Z= 0.185 Angle : 0.531 11.797 20980 Z= 0.262 Chirality : 0.039 0.127 2275 Planarity : 0.003 0.043 2625 Dihedral : 3.753 15.644 2055 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.51 % Allowed : 20.44 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1820 helix: 1.29 (0.16), residues: 1145 sheet: None (None), residues: 0 loop : -0.58 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.003 0.001 HIS B 91 PHE 0.016 0.001 PHE D 276 TYR 0.031 0.001 TYR E 68 ARG 0.007 0.000 ARG C 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5661.23 seconds wall clock time: 100 minutes 26.01 seconds (6026.01 seconds total)