Starting phenix.real_space_refine on Mon Dec 30 04:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y5g_10696/12_2024/6y5g_10696.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y5g_10696/12_2024/6y5g_10696.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/cci-nas-00/data/ceres_data/6y5g_10696/12_2024/6y5g_10696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y5g_10696/12_2024/6y5g_10696.map" model { file = "/net/cci-nas-00/data/ceres_data/6y5g_10696/12_2024/6y5g_10696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y5g_10696/12_2024/6y5g_10696.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= 0.003 sd= 0.245 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7482 2.51 5 N 2058 2.21 5 O 2439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12036 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2454 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1399 Classifications: {'peptide': 172} Link IDs: {'TRANS': 171} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.16, per 1000 atoms: 0.68 Number of scatterers: 12036 At special positions: 0 Unit cell: (87.2, 87.2, 150.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2439 8.00 N 2058 7.00 C 7482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.09 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.93 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.09 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 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 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 38 " " NAG A 410 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 38 " " NAG C 410 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 38 " " NAG E 410 " - " ASN E 81 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 285 " " NAG I 1 " - " ASN B 154 " " NAG J 1 " - " ASN C 165 " " NAG K 1 " - " ASN C 285 " " NAG L 1 " - " ASN E 165 " " NAG M 1 " - " ASN E 285 " " NAG N 1 " - " ASN D 154 " " NAG O 1 " - " ASN F 154 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 24.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 56 removed outlier: 3.578A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 126 removed outlier: 3.690A pdb=" N TYR B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.804A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 188 through 193 removed outlier: 3.930A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 56 removed outlier: 3.579A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 126 removed outlier: 3.690A pdb=" N TYR D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER D 151 " --> pdb=" O ALA D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.578A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 126 removed outlier: 3.689A pdb=" N TYR F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.676A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER F 151 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.131A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'D' and resid 22 through 27 removed outlier: 3.603A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB7, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB8, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.130A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC6, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AC7, first strand: chain 'F' and resid 22 through 27 removed outlier: 3.815A pdb=" N ILE F 140 " --> pdb=" O ALA E 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC9, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'E' and resid 51 through 52 removed outlier: 6.341A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.130A pdb=" N PHE E 87 " --> pdb=" O MET E 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.784A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.968A pdb=" N CYS E 139 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 146 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY E 144 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD9, first strand: chain 'E' and resid 286 through 287 414 hydrogen bonds defined for protein. 1143 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: 4.00 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3966 1.34 - 1.46: 2924 1.46 - 1.58: 5308 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 12276 Sorted by residual: bond pdb=" N ILE B 10 " pdb=" CA ILE B 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.13e+00 bond pdb=" N ILE F 10 " pdb=" CA ILE F 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N ILE D 10 " pdb=" CA ILE D 10 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 9.04e+00 bond pdb=" N GLU D 11 " pdb=" CA GLU D 11 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.98e+00 bond pdb=" N GLU F 11 " pdb=" CA GLU F 11 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.96e+00 ... (remaining 12271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 15794 1.33 - 2.67: 717 2.67 - 4.00: 83 4.00 - 5.34: 32 5.34 - 6.67: 21 Bond angle restraints: 16647 Sorted by residual: angle pdb=" CA LYS D 39 " pdb=" CB LYS D 39 " pdb=" CG LYS D 39 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.28e+00 angle pdb=" CA LYS B 39 " pdb=" CB LYS B 39 " pdb=" CG LYS B 39 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" CA LYS F 39 " pdb=" CB LYS F 39 " pdb=" CG LYS F 39 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.11e+00 angle pdb=" O GLU B 85 " pdb=" C GLU B 85 " pdb=" N ASP B 86 " ideal model delta sigma weight residual 122.07 124.70 -2.63 1.03e+00 9.43e-01 6.53e+00 angle pdb=" O GLU F 85 " pdb=" C GLU F 85 " pdb=" N ASP F 86 " ideal model delta sigma weight residual 122.07 124.66 -2.59 1.03e+00 9.43e-01 6.31e+00 ... (remaining 16642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.13: 7287 22.13 - 44.27: 411 44.27 - 66.40: 72 66.40 - 88.53: 42 88.53 - 110.66: 15 Dihedral angle restraints: 7827 sinusoidal: 3609 harmonic: 4218 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.60 -79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.61 -79.39 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -6.64 -79.36 1 1.00e+01 1.00e-02 7.83e+01 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 1920 0.314 - 0.627: 6 0.627 - 0.941: 3 0.941 - 1.255: 3 1.255 - 1.568: 3 Chirality restraints: 1935 Sorted by residual: chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.15e+03 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-02 2.50e+03 6.13e+03 ... (remaining 1932 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 73 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 74 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 73 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO E 74 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 73 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO C 74 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.026 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 886 2.73 - 3.27: 10349 3.27 - 3.82: 18279 3.82 - 4.36: 22695 4.36 - 4.90: 40185 Nonbonded interactions: 92394 Sorted by model distance: nonbonded pdb=" N GLY D 1 " pdb=" OD2 ASP D 112 " model vdw 2.189 3.120 nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.189 3.120 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.189 3.120 nonbonded pdb=" OE1 GLU F 131 " pdb=" OH TYR F 141 " model vdw 2.280 3.040 nonbonded pdb=" OE1 GLU B 131 " pdb=" OH TYR B 141 " model vdw 2.280 3.040 ... (remaining 92389 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 6.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.300 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.033 12276 Z= 0.343 Angle : 0.661 6.670 16647 Z= 0.345 Chirality : 0.101 1.568 1935 Planarity : 0.004 0.047 2130 Dihedral : 15.738 110.663 5067 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.94 % Allowed : 12.65 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.94 (0.18), residues: 1458 helix: -0.38 (0.26), residues: 366 sheet: -1.23 (0.33), residues: 228 loop : -3.05 (0.15), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 PHE 0.013 0.001 PHE F 9 TYR 0.010 0.001 TYR E 161 ARG 0.002 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 111 LEU cc_start: 0.8585 (tt) cc_final: 0.8270 (tp) REVERT: A 119 GLU cc_start: 0.8087 (tt0) cc_final: 0.7866 (tt0) REVERT: B 46 ASP cc_start: 0.7800 (m-30) cc_final: 0.7480 (m-30) REVERT: C 62 ILE cc_start: 0.8819 (mt) cc_final: 0.8579 (mp) REVERT: C 82 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8093 (mm-30) REVERT: E 27 LYS cc_start: 0.8307 (mttt) cc_final: 0.7933 (mtmm) REVERT: E 111 LEU cc_start: 0.8684 (tt) cc_final: 0.8319 (tt) REVERT: E 119 GLU cc_start: 0.8184 (tt0) cc_final: 0.7955 (tt0) REVERT: E 139 CYS cc_start: 0.7879 (t) cc_final: 0.7368 (t) REVERT: D 49 ASN cc_start: 0.7872 (m-40) cc_final: 0.7542 (m-40) REVERT: D 62 LYS cc_start: 0.8304 (mttt) cc_final: 0.7958 (mmtt) REVERT: D 115 MET cc_start: 0.8653 (tpt) cc_final: 0.8397 (mmm) REVERT: D 121 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7449 (ttmm) REVERT: D 139 LYS cc_start: 0.8239 (tttp) cc_final: 0.7941 (tptm) REVERT: F 115 MET cc_start: 0.8851 (tpt) cc_final: 0.8648 (mmm) REVERT: F 139 LYS cc_start: 0.8220 (tttp) cc_final: 0.7976 (tptm) REVERT: F 168 ASN cc_start: 0.7901 (t0) cc_final: 0.7488 (m-40) outliers start: 12 outliers final: 0 residues processed: 237 average time/residue: 1.4776 time to fit residues: 375.0159 Evaluate side-chains 166 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 125 GLN C 33 GLN C 216 ASN E 17 HIS E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN D 125 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12276 Z= 0.359 Angle : 0.646 7.047 16647 Z= 0.331 Chirality : 0.049 0.218 1935 Planarity : 0.005 0.049 2130 Dihedral : 10.794 92.907 2322 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.43 % Allowed : 14.91 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.99 (0.19), residues: 1458 helix: 0.59 (0.28), residues: 375 sheet: -0.72 (0.33), residues: 234 loop : -2.54 (0.16), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS A 75 PHE 0.021 0.002 PHE D 9 TYR 0.013 0.002 TYR C 308 ARG 0.007 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7027 (tm-30) REVERT: A 77 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6884 (t0) REVERT: A 111 LEU cc_start: 0.8659 (tt) cc_final: 0.8363 (tp) REVERT: A 119 GLU cc_start: 0.8049 (tt0) cc_final: 0.7841 (tt0) REVERT: A 321 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7654 (ttt180) REVERT: B 54 ARG cc_start: 0.7950 (tpt90) cc_final: 0.5599 (tmt-80) REVERT: B 72 GLU cc_start: 0.7482 (mp0) cc_final: 0.7078 (mp0) REVERT: C 41 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: C 62 ILE cc_start: 0.8814 (mt) cc_final: 0.8549 (mp) REVERT: C 82 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8151 (mm-30) REVERT: C 321 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7562 (ttt180) REVERT: E 27 LYS cc_start: 0.8395 (mttt) cc_final: 0.7974 (mtmm) REVERT: E 41 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: E 70 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8282 (tp) REVERT: E 111 LEU cc_start: 0.8635 (tt) cc_final: 0.8317 (tt) REVERT: E 139 CYS cc_start: 0.7734 (t) cc_final: 0.7242 (t) REVERT: E 321 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7502 (ttt180) REVERT: D 49 ASN cc_start: 0.7962 (m-40) cc_final: 0.7647 (m-40) REVERT: D 62 LYS cc_start: 0.8245 (mttt) cc_final: 0.7943 (mmtt) REVERT: D 115 MET cc_start: 0.8789 (tpt) cc_final: 0.8533 (mmm) REVERT: D 121 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7409 (ttmm) REVERT: D 139 LYS cc_start: 0.8296 (tttp) cc_final: 0.7937 (tptm) REVERT: F 37 ASP cc_start: 0.7895 (t0) cc_final: 0.7656 (t70) REVERT: F 115 MET cc_start: 0.8864 (tpt) cc_final: 0.8487 (mmm) REVERT: F 160 ASP cc_start: 0.8034 (m-30) cc_final: 0.7801 (m-30) REVERT: F 168 ASN cc_start: 0.7948 (t0) cc_final: 0.7472 (m-40) outliers start: 44 outliers final: 17 residues processed: 206 average time/residue: 1.4197 time to fit residues: 314.7378 Evaluate side-chains 182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 chunk 105 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12276 Z= 0.257 Angle : 0.595 9.951 16647 Z= 0.311 Chirality : 0.047 0.252 1935 Planarity : 0.004 0.038 2130 Dihedral : 9.914 87.966 2322 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.98 % Allowed : 15.93 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.37 (0.20), residues: 1458 helix: 1.36 (0.29), residues: 357 sheet: -0.01 (0.40), residues: 174 loop : -2.18 (0.16), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE B 9 TYR 0.008 0.001 TYR E 161 ARG 0.007 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: A 77 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6956 (t0) REVERT: A 111 LEU cc_start: 0.8647 (tt) cc_final: 0.8356 (tp) REVERT: A 119 GLU cc_start: 0.8034 (tt0) cc_final: 0.7820 (tt0) REVERT: A 280 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: A 321 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7648 (ttt180) REVERT: B 54 ARG cc_start: 0.7872 (tpt90) cc_final: 0.5489 (tmt-80) REVERT: B 72 GLU cc_start: 0.7369 (mp0) cc_final: 0.7014 (mp0) REVERT: B 123 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7748 (ttp80) REVERT: C 62 ILE cc_start: 0.8687 (mt) cc_final: 0.8406 (mp) REVERT: C 82 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 321 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7669 (ttt180) REVERT: E 27 LYS cc_start: 0.8384 (mttt) cc_final: 0.7966 (mtmm) REVERT: E 31 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6656 (t0) REVERT: E 41 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: E 111 LEU cc_start: 0.8647 (tt) cc_final: 0.8337 (tt) REVERT: E 321 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7509 (ttt180) REVERT: D 38 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7524 (mt) REVERT: D 49 ASN cc_start: 0.7928 (m-40) cc_final: 0.7584 (m-40) REVERT: D 62 LYS cc_start: 0.8247 (mttt) cc_final: 0.7951 (mmtt) REVERT: D 120 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: D 139 LYS cc_start: 0.8386 (tttp) cc_final: 0.7951 (tptm) REVERT: F 115 MET cc_start: 0.8875 (tpt) cc_final: 0.8531 (mmm) REVERT: F 121 LYS cc_start: 0.7900 (ttpt) cc_final: 0.7429 (tttp) REVERT: F 139 LYS cc_start: 0.8442 (tttm) cc_final: 0.8164 (tptm) REVERT: F 160 ASP cc_start: 0.8073 (m-30) cc_final: 0.7854 (m-30) REVERT: F 168 ASN cc_start: 0.7951 (t0) cc_final: 0.7446 (m-40) outliers start: 51 outliers final: 18 residues processed: 196 average time/residue: 1.4461 time to fit residues: 304.3592 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12276 Z= 0.306 Angle : 0.643 20.418 16647 Z= 0.331 Chirality : 0.049 0.324 1935 Planarity : 0.004 0.051 2130 Dihedral : 8.933 78.660 2322 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.14 % Allowed : 16.71 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.19 (0.20), residues: 1458 helix: 1.52 (0.28), residues: 354 sheet: -0.02 (0.36), residues: 204 loop : -2.09 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 75 PHE 0.020 0.002 PHE D 9 TYR 0.012 0.002 TYR A 195 ARG 0.009 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 157 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: A 77 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6939 (t0) REVERT: A 111 LEU cc_start: 0.8669 (tt) cc_final: 0.8387 (tp) REVERT: A 119 GLU cc_start: 0.8062 (tt0) cc_final: 0.7855 (tt0) REVERT: A 280 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: B 72 GLU cc_start: 0.7405 (mp0) cc_final: 0.6979 (mp0) REVERT: C 41 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: C 70 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8204 (tp) REVERT: C 73 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7733 (t70) REVERT: C 82 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8081 (mm-30) REVERT: C 321 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7689 (ttt180) REVERT: E 27 LYS cc_start: 0.8411 (mttt) cc_final: 0.8011 (mtmm) REVERT: E 31 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6777 (t0) REVERT: E 41 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: E 70 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8268 (tp) REVERT: E 111 LEU cc_start: 0.8662 (tt) cc_final: 0.8362 (tt) REVERT: E 321 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7514 (ttt180) REVERT: D 38 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7579 (mt) REVERT: D 49 ASN cc_start: 0.7947 (m-40) cc_final: 0.7625 (m-40) REVERT: D 62 LYS cc_start: 0.8238 (mttt) cc_final: 0.7965 (mmtt) REVERT: D 120 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: D 139 LYS cc_start: 0.8443 (tttp) cc_final: 0.8040 (tptm) REVERT: F 115 MET cc_start: 0.8848 (tpt) cc_final: 0.8481 (mmm) REVERT: F 160 ASP cc_start: 0.8079 (m-30) cc_final: 0.7857 (m-30) REVERT: F 168 ASN cc_start: 0.8090 (t0) cc_final: 0.7491 (m-40) outliers start: 53 outliers final: 20 residues processed: 188 average time/residue: 1.4434 time to fit residues: 292.5213 Evaluate side-chains 182 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 124 optimal weight: 0.0470 chunk 35 optimal weight: 0.5980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN E 295 GLN D 28 ASN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12276 Z= 0.218 Angle : 0.612 20.605 16647 Z= 0.316 Chirality : 0.048 0.351 1935 Planarity : 0.004 0.036 2130 Dihedral : 8.070 69.640 2322 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.06 % Allowed : 17.25 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.02 (0.20), residues: 1458 helix: 1.69 (0.29), residues: 360 sheet: 0.11 (0.36), residues: 204 loop : -2.02 (0.16), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 234 HIS 0.003 0.001 HIS A 75 PHE 0.015 0.001 PHE D 9 TYR 0.008 0.001 TYR A 195 ARG 0.008 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6950 (t0) REVERT: A 111 LEU cc_start: 0.8642 (tt) cc_final: 0.8388 (tp) REVERT: A 280 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7607 (mm-30) REVERT: B 72 GLU cc_start: 0.7294 (mp0) cc_final: 0.6980 (mp0) REVERT: C 70 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8178 (tp) REVERT: C 73 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7606 (t70) REVERT: C 82 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 321 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7690 (ttt180) REVERT: E 27 LYS cc_start: 0.8412 (mttt) cc_final: 0.7998 (mtmm) REVERT: E 41 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: E 70 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8412 (tp) REVERT: E 111 LEU cc_start: 0.8682 (tt) cc_final: 0.8399 (tt) REVERT: E 321 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7522 (ttt180) REVERT: D 38 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7533 (mt) REVERT: D 49 ASN cc_start: 0.7843 (m-40) cc_final: 0.7512 (m-40) REVERT: D 62 LYS cc_start: 0.8232 (mttt) cc_final: 0.7970 (mmtt) REVERT: D 121 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7336 (ttpt) REVERT: D 139 LYS cc_start: 0.8297 (tttp) cc_final: 0.7943 (tptm) REVERT: F 115 MET cc_start: 0.8881 (tpt) cc_final: 0.8488 (mmm) REVERT: F 123 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7521 (ttp80) REVERT: F 139 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8147 (tptm) REVERT: F 160 ASP cc_start: 0.8048 (m-30) cc_final: 0.7835 (m-30) REVERT: F 168 ASN cc_start: 0.8085 (t0) cc_final: 0.7513 (m-40) outliers start: 52 outliers final: 20 residues processed: 188 average time/residue: 1.4543 time to fit residues: 294.3386 Evaluate side-chains 181 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12276 Z= 0.341 Angle : 0.677 16.460 16647 Z= 0.349 Chirality : 0.051 0.356 1935 Planarity : 0.004 0.036 2130 Dihedral : 7.618 62.892 2322 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.14 % Allowed : 17.33 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.02 (0.20), residues: 1458 helix: 1.71 (0.28), residues: 354 sheet: 0.09 (0.36), residues: 204 loop : -1.99 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 234 HIS 0.004 0.001 HIS A 75 PHE 0.020 0.002 PHE D 9 TYR 0.010 0.002 TYR C 308 ARG 0.009 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: A 77 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6974 (t0) REVERT: A 111 LEU cc_start: 0.8693 (tt) cc_final: 0.8429 (tp) REVERT: A 280 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: B 72 GLU cc_start: 0.7312 (mp0) cc_final: 0.6932 (mp0) REVERT: C 70 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8272 (tp) REVERT: C 73 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7726 (t70) REVERT: C 321 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7665 (ttt180) REVERT: E 27 LYS cc_start: 0.8414 (mttt) cc_final: 0.7998 (mtmm) REVERT: E 41 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: E 70 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8252 (tp) REVERT: E 111 LEU cc_start: 0.8673 (tt) cc_final: 0.8384 (tt) REVERT: E 321 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7535 (ttt180) REVERT: D 38 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7577 (mt) REVERT: D 49 ASN cc_start: 0.7956 (m-40) cc_final: 0.7646 (m-40) REVERT: D 62 LYS cc_start: 0.8254 (mttt) cc_final: 0.8018 (mmtt) REVERT: D 121 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7397 (ttpt) REVERT: D 139 LYS cc_start: 0.8383 (tttp) cc_final: 0.8116 (tptm) REVERT: D 168 ASN cc_start: 0.8126 (t0) cc_final: 0.7411 (t0) REVERT: F 115 MET cc_start: 0.8874 (tpt) cc_final: 0.8455 (mmm) REVERT: F 139 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8202 (tptm) REVERT: F 160 ASP cc_start: 0.8113 (m-30) cc_final: 0.7898 (m-30) REVERT: F 168 ASN cc_start: 0.8129 (t0) cc_final: 0.7498 (m-40) outliers start: 53 outliers final: 29 residues processed: 185 average time/residue: 1.4274 time to fit residues: 284.8316 Evaluate side-chains 191 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12276 Z= 0.288 Angle : 0.655 19.852 16647 Z= 0.337 Chirality : 0.049 0.363 1935 Planarity : 0.004 0.048 2130 Dihedral : 7.236 55.570 2322 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.83 % Allowed : 17.72 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.96 (0.20), residues: 1458 helix: 1.79 (0.28), residues: 354 sheet: 0.13 (0.36), residues: 204 loop : -1.98 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.004 0.001 HIS A 75 PHE 0.017 0.002 PHE D 9 TYR 0.008 0.002 TYR A 195 ARG 0.010 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: A 77 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6971 (t0) REVERT: A 111 LEU cc_start: 0.8702 (tt) cc_final: 0.8465 (tp) REVERT: A 280 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: B 72 GLU cc_start: 0.7302 (mp0) cc_final: 0.6921 (mp0) REVERT: C 31 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: C 41 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: C 70 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8206 (tp) REVERT: C 73 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7651 (t70) REVERT: C 321 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7637 (ttt180) REVERT: E 27 LYS cc_start: 0.8407 (mttt) cc_final: 0.7980 (mtmm) REVERT: E 41 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: E 70 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8380 (tp) REVERT: E 111 LEU cc_start: 0.8686 (tt) cc_final: 0.8395 (tt) REVERT: E 321 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7556 (ttt180) REVERT: D 38 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7548 (mt) REVERT: D 49 ASN cc_start: 0.7944 (m-40) cc_final: 0.7644 (m-40) REVERT: D 62 LYS cc_start: 0.8258 (mttt) cc_final: 0.8006 (mmtt) REVERT: D 72 GLU cc_start: 0.7491 (mp0) cc_final: 0.6905 (mp0) REVERT: D 121 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7409 (ttpt) REVERT: D 139 LYS cc_start: 0.8338 (tttp) cc_final: 0.8043 (tptm) REVERT: D 168 ASN cc_start: 0.8111 (t0) cc_final: 0.7409 (t0) REVERT: F 57 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6633 (pt0) REVERT: F 115 MET cc_start: 0.8873 (tpt) cc_final: 0.8465 (mmm) REVERT: F 121 LYS cc_start: 0.7805 (tttt) cc_final: 0.7366 (tttp) REVERT: F 139 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8285 (tptm) REVERT: F 160 ASP cc_start: 0.8067 (m-30) cc_final: 0.7859 (m-30) REVERT: F 168 ASN cc_start: 0.8113 (t0) cc_final: 0.7483 (m-40) outliers start: 49 outliers final: 25 residues processed: 185 average time/residue: 1.3762 time to fit residues: 274.2995 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12276 Z= 0.265 Angle : 0.643 17.400 16647 Z= 0.332 Chirality : 0.049 0.366 1935 Planarity : 0.004 0.045 2130 Dihedral : 7.030 52.042 2322 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.51 % Allowed : 18.66 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.89 (0.20), residues: 1458 helix: 1.85 (0.28), residues: 354 sheet: 0.15 (0.36), residues: 204 loop : -1.93 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.003 0.001 HIS A 75 PHE 0.016 0.002 PHE D 9 TYR 0.008 0.001 TYR C 308 ARG 0.010 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: A 77 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6978 (t0) REVERT: A 111 LEU cc_start: 0.8700 (tt) cc_final: 0.8463 (tp) REVERT: A 280 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: B 72 GLU cc_start: 0.7250 (mp0) cc_final: 0.6875 (mp0) REVERT: C 31 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6863 (t70) REVERT: C 41 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: C 70 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8204 (tp) REVERT: C 73 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7634 (t70) REVERT: C 77 ASP cc_start: 0.7358 (m-30) cc_final: 0.7074 (t0) REVERT: C 321 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7639 (ttt180) REVERT: E 27 LYS cc_start: 0.8380 (mttt) cc_final: 0.7953 (mtmm) REVERT: E 41 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: E 70 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8373 (tp) REVERT: E 111 LEU cc_start: 0.8693 (tt) cc_final: 0.8403 (tt) REVERT: E 321 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: D 38 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7539 (mt) REVERT: D 49 ASN cc_start: 0.7942 (m-40) cc_final: 0.7644 (m-40) REVERT: D 62 LYS cc_start: 0.8233 (mttt) cc_final: 0.7977 (mmtt) REVERT: D 72 GLU cc_start: 0.7460 (mp0) cc_final: 0.6870 (mp0) REVERT: D 121 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7343 (ttpt) REVERT: D 139 LYS cc_start: 0.8301 (tttp) cc_final: 0.8021 (tptm) REVERT: D 168 ASN cc_start: 0.8108 (t0) cc_final: 0.7400 (t0) REVERT: F 57 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6591 (pt0) REVERT: F 115 MET cc_start: 0.8870 (tpt) cc_final: 0.8450 (mmm) REVERT: F 121 LYS cc_start: 0.7834 (tttt) cc_final: 0.7392 (tttp) REVERT: F 139 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8198 (tptm) REVERT: F 160 ASP cc_start: 0.8058 (m-30) cc_final: 0.7848 (m-30) REVERT: F 168 ASN cc_start: 0.8101 (t0) cc_final: 0.7486 (m-40) outliers start: 45 outliers final: 27 residues processed: 183 average time/residue: 1.4377 time to fit residues: 283.3422 Evaluate side-chains 190 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12276 Z= 0.321 Angle : 0.676 17.289 16647 Z= 0.348 Chirality : 0.050 0.352 1935 Planarity : 0.004 0.042 2130 Dihedral : 6.992 49.999 2322 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.75 % Allowed : 18.27 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.94 (0.20), residues: 1458 helix: 1.75 (0.28), residues: 354 sheet: 0.01 (0.33), residues: 255 loop : -2.01 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 234 HIS 0.004 0.001 HIS C 75 PHE 0.019 0.002 PHE D 9 TYR 0.010 0.002 TYR C 308 ARG 0.009 0.001 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 77 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6977 (t0) REVERT: A 111 LEU cc_start: 0.8711 (tt) cc_final: 0.8475 (tp) REVERT: A 280 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: B 72 GLU cc_start: 0.7240 (mp0) cc_final: 0.6878 (mp0) REVERT: C 31 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6989 (t0) REVERT: C 41 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: C 70 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8251 (tp) REVERT: C 73 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7710 (t70) REVERT: C 77 ASP cc_start: 0.7399 (m-30) cc_final: 0.7099 (t0) REVERT: C 321 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7626 (ttt180) REVERT: E 27 LYS cc_start: 0.8381 (mttt) cc_final: 0.7954 (mtmm) REVERT: E 41 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: E 70 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8253 (tp) REVERT: E 111 LEU cc_start: 0.8684 (tt) cc_final: 0.8396 (tt) REVERT: E 321 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7557 (ttt180) REVERT: D 38 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7560 (mt) REVERT: D 49 ASN cc_start: 0.7951 (m-40) cc_final: 0.7654 (m-40) REVERT: D 62 LYS cc_start: 0.8269 (mttt) cc_final: 0.8032 (mmtt) REVERT: D 72 GLU cc_start: 0.7459 (mp0) cc_final: 0.6864 (mp0) REVERT: D 139 LYS cc_start: 0.8320 (tttp) cc_final: 0.7995 (tptm) REVERT: D 168 ASN cc_start: 0.8116 (t0) cc_final: 0.7398 (t0) REVERT: F 57 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6651 (pt0) REVERT: F 115 MET cc_start: 0.8796 (tpt) cc_final: 0.8405 (mmm) REVERT: F 121 LYS cc_start: 0.7850 (tttt) cc_final: 0.7393 (tttp) REVERT: F 160 ASP cc_start: 0.8017 (m-30) cc_final: 0.7806 (m-30) REVERT: F 168 ASN cc_start: 0.8174 (t0) cc_final: 0.7490 (m-40) outliers start: 48 outliers final: 27 residues processed: 179 average time/residue: 1.3812 time to fit residues: 266.7708 Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12276 Z= 0.295 Angle : 0.664 17.816 16647 Z= 0.342 Chirality : 0.049 0.371 1935 Planarity : 0.004 0.042 2130 Dihedral : 6.889 48.007 2322 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.43 % Allowed : 18.58 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.90 (0.20), residues: 1458 helix: 1.79 (0.28), residues: 354 sheet: 0.02 (0.33), residues: 255 loop : -1.98 (0.17), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 234 HIS 0.004 0.001 HIS A 75 PHE 0.017 0.002 PHE D 9 TYR 0.009 0.002 TYR C 308 ARG 0.009 0.001 ARG E 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: A 77 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6978 (t0) REVERT: A 111 LEU cc_start: 0.8704 (tt) cc_final: 0.8467 (tp) REVERT: A 280 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: B 72 GLU cc_start: 0.7202 (mp0) cc_final: 0.6892 (mp0) REVERT: C 31 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6984 (t0) REVERT: C 41 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: C 70 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8208 (tp) REVERT: C 73 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7726 (t70) REVERT: C 77 ASP cc_start: 0.7381 (m-30) cc_final: 0.7092 (t0) REVERT: C 321 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7629 (ttt180) REVERT: E 27 LYS cc_start: 0.8381 (mttt) cc_final: 0.7951 (mtmm) REVERT: E 41 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: E 70 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8369 (tp) REVERT: E 111 LEU cc_start: 0.8679 (tt) cc_final: 0.8390 (tt) REVERT: E 321 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: D 38 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7546 (mt) REVERT: D 49 ASN cc_start: 0.7944 (m-40) cc_final: 0.7660 (m-40) REVERT: D 62 LYS cc_start: 0.8250 (mttt) cc_final: 0.8019 (mmtt) REVERT: D 72 GLU cc_start: 0.7424 (mp0) cc_final: 0.6840 (mp0) REVERT: D 139 LYS cc_start: 0.8318 (tttp) cc_final: 0.7983 (tptm) REVERT: D 168 ASN cc_start: 0.8090 (t0) cc_final: 0.7386 (t0) REVERT: F 57 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6605 (pt0) REVERT: F 115 MET cc_start: 0.8872 (tpt) cc_final: 0.8448 (mmm) REVERT: F 121 LYS cc_start: 0.7846 (tttt) cc_final: 0.7387 (tttp) REVERT: F 139 LYS cc_start: 0.8470 (tttm) cc_final: 0.7999 (tptm) REVERT: F 160 ASP cc_start: 0.8018 (m-30) cc_final: 0.7804 (m-30) REVERT: F 168 ASN cc_start: 0.8113 (t0) cc_final: 0.7483 (m-40) outliers start: 44 outliers final: 30 residues processed: 182 average time/residue: 1.3883 time to fit residues: 272.3938 Evaluate side-chains 194 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 321 ARG Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 195 TYR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 277 CYS Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 143 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 295 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN E 295 GLN D 78 GLN F 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.119837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.102031 restraints weight = 14241.255| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.88 r_work: 0.2937 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12276 Z= 0.187 Angle : 0.590 14.995 16647 Z= 0.306 Chirality : 0.046 0.316 1935 Planarity : 0.004 0.036 2130 Dihedral : 6.511 49.421 2322 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.36 % Allowed : 18.89 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1458 helix: 2.04 (0.29), residues: 357 sheet: 0.23 (0.35), residues: 225 loop : -1.87 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 234 HIS 0.002 0.001 HIS D 106 PHE 0.012 0.001 PHE E 120 TYR 0.007 0.001 TYR C 105 ARG 0.009 0.000 ARG E 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4738.67 seconds wall clock time: 86 minutes 4.69 seconds (5164.69 seconds total)