Starting phenix.real_space_refine (version: dev) on Mon Feb 20 12:14:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2023/6y5g_10696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2023/6y5g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2023/6y5g_10696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2023/6y5g_10696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2023/6y5g_10696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5g_10696/02_2023/6y5g_10696.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 19": "OD1" <-> "OD2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 101": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 172": "OD1" <-> "OD2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 19": "OD1" <-> "OD2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F ASP 145": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 3 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 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 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: 3 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 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: 3 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 7.35, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 5.07 Conformation dependent library (CDL) restraints added in 1.9 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: 0.80 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: 3.85 Time building geometry restraints manager: 5.45 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: 100.12 - 106.89: 345 106.89 - 113.67: 6977 113.67 - 120.44: 4414 120.44 - 127.22: 4785 127.22 - 133.99: 126 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 - 17.87: 6673 17.87 - 35.73: 500 35.73 - 53.60: 129 53.60 - 71.47: 12 71.47 - 89.33: 27 Dihedral angle restraints: 7341 sinusoidal: 3123 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 7338 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 2.520 nonbonded pdb=" N GLY F 1 " pdb=" OD2 ASP F 112 " model vdw 2.189 2.520 nonbonded pdb=" N GLY B 1 " pdb=" OD2 ASP B 112 " model vdw 2.189 2.520 nonbonded pdb=" OE1 GLU F 131 " pdb=" OH TYR F 141 " model vdw 2.280 2.440 nonbonded pdb=" OE1 GLU B 131 " pdb=" OH TYR B 141 " model vdw 2.280 2.440 ... (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 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.760 Check model and map are aligned: 0.180 Process input model: 34.830 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.120 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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= 0.304 Angle : 0.561 6.670 16647 Z= 0.325 Chirality : 0.099 1.568 1935 Planarity : 0.004 0.047 2130 Dihedral : 14.040 89.331 4581 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 % 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 1.478 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 237 average time/residue: 1.4863 time to fit residues: 377.6863 Evaluate side-chains 159 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.448 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9484 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 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 ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 12276 Z= 0.391 Angle : 0.630 7.130 16647 Z= 0.336 Chirality : 0.049 0.293 1935 Planarity : 0.005 0.049 2130 Dihedral : 5.674 54.667 1836 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 3.51 % 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: -2.03 (0.19), residues: 1458 helix: 0.57 (0.28), residues: 372 sheet: -0.75 (0.33), residues: 228 loop : -2.55 (0.16), residues: 858 *********************** 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 221 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 176 time to evaluate : 1.424 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 198 average time/residue: 1.2920 time to fit residues: 276.7716 Evaluate side-chains 176 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.284 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 0.4613 time to fit residues: 6.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 105 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN C 54 ASN C 216 ASN C 246 ASN E 54 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12276 Z= 0.248 Angle : 0.548 9.959 16647 Z= 0.292 Chirality : 0.046 0.308 1935 Planarity : 0.004 0.040 2130 Dihedral : 5.336 49.647 1836 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 3.59 % 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: -1.40 (0.20), residues: 1458 helix: 1.34 (0.29), residues: 357 sheet: -0.11 (0.39), residues: 174 loop : -2.18 (0.16), residues: 927 *********************** 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 212 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.512 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 26 residues processed: 196 average time/residue: 1.3707 time to fit residues: 290.0857 Evaluate side-chains 174 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.1680 time to fit residues: 3.3320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN C 216 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1965 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= 0.265 Angle : 0.570 12.180 16647 Z= 0.303 Chirality : 0.047 0.304 1935 Planarity : 0.004 0.041 2130 Dihedral : 5.332 48.613 1836 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 3.28 % 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: -1.19 (0.20), residues: 1458 helix: 1.52 (0.29), residues: 357 sheet: 0.04 (0.39), residues: 174 loop : -2.05 (0.16), residues: 927 *********************** 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 190 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 1.544 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 175 average time/residue: 1.3066 time to fit residues: 247.3580 Evaluate side-chains 173 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.4044 time to fit residues: 4.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 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 33 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 12276 Z= 0.267 Angle : 0.618 19.669 16647 Z= 0.326 Chirality : 0.049 0.369 1935 Planarity : 0.004 0.043 2130 Dihedral : 5.456 48.115 1836 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 3.04 % 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: -1.05 (0.20), residues: 1458 helix: 1.65 (0.28), residues: 357 sheet: 0.11 (0.39), residues: 174 loop : -1.96 (0.16), residues: 927 *********************** 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 186 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.529 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 25 residues processed: 178 average time/residue: 1.3600 time to fit residues: 261.7388 Evaluate side-chains 166 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.1935 time to fit residues: 3.3451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 12276 Z= 0.249 Angle : 0.601 15.808 16647 Z= 0.318 Chirality : 0.048 0.340 1935 Planarity : 0.004 0.045 2130 Dihedral : 5.425 47.227 1836 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 3.36 % 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: -0.93 (0.20), residues: 1458 helix: 1.80 (0.29), residues: 357 sheet: 0.07 (0.36), residues: 204 loop : -1.93 (0.17), residues: 897 *********************** 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 184 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 31 residues processed: 173 average time/residue: 1.3519 time to fit residues: 252.9197 Evaluate side-chains 169 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.512 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.2045 time to fit residues: 3.5456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 0.0270 chunk 77 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12276 Z= 0.191 Angle : 0.567 18.527 16647 Z= 0.301 Chirality : 0.046 0.300 1935 Planarity : 0.004 0.047 2130 Dihedral : 5.225 46.317 1836 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 3.28 % 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: -0.79 (0.20), residues: 1458 helix: 1.98 (0.29), residues: 357 sheet: 0.15 (0.36), residues: 204 loop : -1.88 (0.17), residues: 897 *********************** 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 186 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 30 residues processed: 181 average time/residue: 1.2951 time to fit residues: 253.9128 Evaluate side-chains 166 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.2414 time to fit residues: 2.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12276 Z= 0.283 Angle : 0.633 17.761 16647 Z= 0.333 Chirality : 0.049 0.368 1935 Planarity : 0.004 0.045 2130 Dihedral : 5.378 45.914 1836 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 3.20 % 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: -0.82 (0.20), residues: 1458 helix: 1.96 (0.29), residues: 354 sheet: 0.11 (0.36), residues: 204 loop : -1.88 (0.17), residues: 900 *********************** 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 180 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 34 residues processed: 172 average time/residue: 1.3947 time to fit residues: 259.2158 Evaluate side-chains 171 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.479 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 5 average time/residue: 0.6698 time to fit residues: 5.8113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 0.0070 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 12276 Z= 0.258 Angle : 0.623 16.794 16647 Z= 0.328 Chirality : 0.048 0.358 1935 Planarity : 0.004 0.047 2130 Dihedral : 5.427 45.764 1836 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 2.73 % 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: -0.82 (0.21), residues: 1458 helix: 1.98 (0.29), residues: 354 sheet: -0.13 (0.32), residues: 255 loop : -1.90 (0.17), residues: 849 *********************** 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 174 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 34 residues processed: 170 average time/residue: 1.3457 time to fit residues: 248.0734 Evaluate side-chains 170 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.494 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.2343 time to fit residues: 2.9581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12276 Z= 0.218 Angle : 0.588 15.878 16647 Z= 0.311 Chirality : 0.046 0.321 1935 Planarity : 0.004 0.045 2130 Dihedral : 5.323 44.912 1836 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 2.65 % 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: -0.69 (0.21), residues: 1458 helix: 2.09 (0.29), residues: 354 sheet: -0.15 (0.31), residues: 285 loop : -1.85 (0.18), residues: 819 ********************** 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 178 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 31 residues processed: 177 average time/residue: 1.3210 time to fit residues: 253.0669 Evaluate side-chains 171 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 30 residues processed: 1 average time/residue: 1.4009 time to fit residues: 3.3602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.119076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.101584 restraints weight = 14263.686| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.85 r_work: 0.2922 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 12276 Z= 0.235 Angle : 0.598 15.763 16647 Z= 0.316 Chirality : 0.047 0.313 1935 Planarity : 0.004 0.044 2130 Dihedral : 5.401 44.729 1836 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.72 (0.21), residues: 1458 helix: 2.06 (0.29), residues: 354 sheet: -0.16 (0.31), residues: 285 loop : -1.86 (0.18), residues: 819 =============================================================================== Job complete usr+sys time: 4635.60 seconds wall clock time: 84 minutes 21.08 seconds (5061.08 seconds total)