Starting phenix.real_space_refine on Sun Jul 21 23:55:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqw_37756/07_2024/8wqw_37756.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqw_37756/07_2024/8wqw_37756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqw_37756/07_2024/8wqw_37756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqw_37756/07_2024/8wqw_37756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqw_37756/07_2024/8wqw_37756.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wqw_37756/07_2024/8wqw_37756.cif" } resolution = 3.27 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8972 atoms to isotropic. 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 62 5.16 5 C 5607 2.51 5 N 1538 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 151": "OD1" <-> "OD2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "F ASP 61": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8972 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1409 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 8, 'TRANS': 179} Chain breaks: 1 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1686 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 213} Chain: "C" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1626 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2445 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 797 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} 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: "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 Time building chain proxies: 6.60, per 1000 atoms: 0.74 Number of scatterers: 8972 At special positions: 0 Unit cell: (88.32, 82.8, 155.94, 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 62 16.00 O 1765 8.00 N 1538 7.00 C 5607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 629 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 803 " distance=2.03 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS A 656 " - pdb=" SG CYS A 705 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 691 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 771 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 202 " distance=2.04 Simple disulfide: pdb=" SG CYS B 222 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 156 " distance=2.04 Simple disulfide: pdb=" SG CYS D 180 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 206 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS D 258 " - pdb=" SG CYS D 309 " distance=2.05 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 307 " distance=2.03 Simple disulfide: pdb=" SG CYS D 274 " - pdb=" SG CYS D 280 " distance=2.03 Simple disulfide: pdb=" SG CYS D 287 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 98 " 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 ALPHA1-4 " NAG G 2 " - " MAN G 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN D 63 " " NAG H 1 " - " ASN D 33 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.5 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 26 sheets defined 13.3% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 650 through 654 removed outlier: 3.744A pdb=" N GLY A 654 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 4.111A pdb=" N GLY A 697 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 702 removed outlier: 4.017A pdb=" N ALA A 701 " --> pdb=" O CYS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 809 through 817 removed outlier: 3.768A pdb=" N VAL A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 816 " --> pdb=" O ALA A 812 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER A 817 " --> pdb=" O VAL A 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.142A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.249A pdb=" N THR B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 122 through 128 Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.669A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'D' and resid 43 through 52 Processing helix chain 'D' and resid 54 through 64 removed outlier: 3.612A pdb=" N SER D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 removed outlier: 3.546A pdb=" N SER D 78 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 79 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 80 " --> pdb=" O ARG D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 75 through 80' Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.895A pdb=" N TRP D 103 " --> pdb=" O CYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 removed outlier: 4.074A pdb=" N SER D 163 " --> pdb=" O SER D 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 163' Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.998A pdb=" N PHE D 191 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.756A pdb=" N PHE D 256 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.955A pdb=" N ARG E 28 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER E 29 " --> pdb=" O SER E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 29' Processing helix chain 'F' and resid 89 through 93 removed outlier: 4.235A pdb=" N THR F 93 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 628 through 631 removed outlier: 4.093A pdb=" N VAL A 729 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 630 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA A 727 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 628 through 631 removed outlier: 4.093A pdb=" N VAL A 729 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 630 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA A 727 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 641 through 649 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.978A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.660A pdb=" N ALA B 92 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 36 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 126 through 130 removed outlier: 3.631A pdb=" N SER B 126 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 149 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 128 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 147 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 145 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 150 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR B 182 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 130 removed outlier: 3.631A pdb=" N SER B 126 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 149 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 128 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 147 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 145 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 150 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR B 182 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.559A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.687A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 33 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 38 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.610A pdb=" N SER C 114 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN C 137 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 176 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER C 162 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 73 removed outlier: 6.459A pdb=" N LEU D 167 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 83 removed outlier: 3.538A pdb=" N TYR D 83 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE D 129 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE D 175 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU D 131 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LYS D 110 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY D 142 " --> pdb=" O LYS D 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 147 through 148 Processing sheet with id=AB8, first strand: chain 'D' and resid 177 through 180 removed outlier: 3.724A pdb=" N ALA D 179 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 332 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N MET D 338 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE D 208 " --> pdb=" O MET D 338 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR D 340 " --> pdb=" O CYS D 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 177 through 180 removed outlier: 3.724A pdb=" N ALA D 179 " --> pdb=" O TYR D 332 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 332 " --> pdb=" O ALA D 179 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS D 331 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 333 " --> pdb=" O TRP D 229 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP D 229 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 335 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL D 227 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA D 228 " --> pdb=" O MET D 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 244 through 248 removed outlier: 3.606A pdb=" N LYS D 244 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 257 through 258 removed outlier: 3.804A pdb=" N VAL D 257 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 310 " --> pdb=" O VAL D 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.939A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 13 Processing sheet with id=AC5, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.929A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.808A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 50 " --> pdb=" O ASP F 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP F 61 " --> pdb=" O ARG F 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.600A pdb=" N THR F 100 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 112 " --> pdb=" O THR F 100 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 729 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2909 1.34 - 1.47: 2347 1.47 - 1.60: 3842 1.60 - 1.73: 1 1.73 - 1.85: 77 Bond restraints: 9176 Sorted by residual: bond pdb=" CG PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 1.503 1.213 0.290 3.40e-02 8.65e+02 7.26e+01 bond pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 1.473 1.514 -0.041 1.40e-02 5.10e+03 8.76e+00 bond pdb=" CB PRO F 41 " pdb=" CG PRO F 41 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.09e+00 bond pdb=" C5 MAN G 3 " pdb=" O5 MAN G 3 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" C1 MAN G 3 " pdb=" C2 MAN G 3 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.87e+00 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 85.55 - 95.24: 2 95.24 - 104.93: 164 104.93 - 114.63: 5455 114.63 - 124.32: 6574 124.32 - 134.01: 235 Bond angle restraints: 12430 Sorted by residual: angle pdb=" N PRO F 41 " pdb=" CD PRO F 41 " pdb=" CG PRO F 41 " ideal model delta sigma weight residual 103.20 85.55 17.65 1.50e+00 4.44e-01 1.38e+02 angle pdb=" CA PRO F 41 " pdb=" N PRO F 41 " pdb=" CD PRO F 41 " ideal model delta sigma weight residual 112.00 101.86 10.14 1.40e+00 5.10e-01 5.25e+01 angle pdb=" CA PRO F 41 " pdb=" CB PRO F 41 " pdb=" CG PRO F 41 " ideal model delta sigma weight residual 104.50 92.65 11.85 1.90e+00 2.77e-01 3.89e+01 angle pdb=" C GLU B 154 " pdb=" N PRO B 155 " pdb=" CD PRO B 155 " ideal model delta sigma weight residual 120.60 110.84 9.76 2.20e+00 2.07e-01 1.97e+01 angle pdb=" N PRO F 41 " pdb=" CA PRO F 41 " pdb=" CB PRO F 41 " ideal model delta sigma weight residual 103.25 100.04 3.21 1.05e+00 9.07e-01 9.36e+00 ... (remaining 12425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 5297 24.37 - 48.73: 234 48.73 - 73.10: 26 73.10 - 97.47: 11 97.47 - 121.84: 1 Dihedral angle restraints: 5569 sinusoidal: 2237 harmonic: 3332 Sorted by residual: dihedral pdb=" CB CYS D 258 " pdb=" SG CYS D 258 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual 93.00 38.10 54.90 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS A 629 " pdb=" SG CYS A 629 " pdb=" SG CYS A 725 " pdb=" CB CYS A 725 " ideal model delta sinusoidal sigma weight residual -86.00 -128.61 42.61 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS A 644 " pdb=" SG CYS A 644 " pdb=" SG CYS A 803 " pdb=" CB CYS A 803 " ideal model delta sinusoidal sigma weight residual -86.00 -128.55 42.55 1 1.00e+01 1.00e-02 2.53e+01 ... (remaining 5566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1295 0.099 - 0.198: 67 0.198 - 0.297: 1 0.297 - 0.396: 0 0.396 - 0.494: 2 Chirality restraints: 1365 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 33 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN D 63 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CB ILE B 201 " pdb=" CA ILE B 201 " pdb=" CG1 ILE B 201 " pdb=" CG2 ILE B 201 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1362 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 154 " -0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO B 155 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 40 " -0.064 5.00e-02 4.00e+02 9.03e-02 1.31e+01 pdb=" N PRO F 41 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO F 41 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 41 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " 0.021 2.00e-02 2.50e+03 1.77e-02 7.81e+00 pdb=" CG TRP B 36 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " 0.001 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 193 2.68 - 3.24: 8295 3.24 - 3.79: 13011 3.79 - 4.35: 17620 4.35 - 4.90: 29036 Nonbonded interactions: 68155 Sorted by model distance: nonbonded pdb=" OG SER E 33 " pdb=" OD1 ASN E 88 " model vdw 2.125 2.440 nonbonded pdb=" O HIS C 189 " pdb=" NH2 ARG C 211 " model vdw 2.174 2.520 nonbonded pdb=" NH2 ARG B 98 " pdb=" OD2 ASP B 107 " model vdw 2.207 2.520 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER C 208 " model vdw 2.258 2.520 nonbonded pdb=" NE2 HIS D 243 " pdb=" OH TYR D 332 " model vdw 2.265 2.520 ... (remaining 68150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 11.850 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.110 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 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 0.290 9176 Z= 0.333 Angle : 0.700 17.651 12430 Z= 0.378 Chirality : 0.048 0.494 1365 Planarity : 0.006 0.095 1594 Dihedral : 13.416 121.836 3376 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1158 helix: -1.46 (0.51), residues: 80 sheet: 0.03 (0.26), residues: 382 loop : -0.85 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 36 HIS 0.004 0.001 HIS D 56 PHE 0.014 0.002 PHE D 130 TYR 0.015 0.002 TYR F 97 ARG 0.006 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5315 (m-80) cc_final: 0.5070 (m-80) REVERT: A 641 ARG cc_start: 0.6523 (mpt90) cc_final: 0.6205 (mpt90) REVERT: A 720 TRP cc_start: 0.6351 (m-10) cc_final: 0.5939 (m-90) REVERT: A 797 ARG cc_start: 0.7707 (mtt90) cc_final: 0.7264 (mpt180) REVERT: B 29 PHE cc_start: 0.7817 (t80) cc_final: 0.7517 (t80) REVERT: C 127 SER cc_start: 0.7704 (m) cc_final: 0.7235 (p) REVERT: C 185 ASP cc_start: 0.8376 (m-30) cc_final: 0.8110 (p0) REVERT: D 131 GLU cc_start: 0.7104 (pp20) cc_final: 0.6828 (pp20) REVERT: D 136 ASP cc_start: 0.8078 (p0) cc_final: 0.7767 (p0) REVERT: D 268 GLU cc_start: 0.6697 (pp20) cc_final: 0.6213 (pp20) REVERT: D 270 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7472 (mt-10) REVERT: D 332 TYR cc_start: 0.7177 (t80) cc_final: 0.6742 (t80) outliers start: 1 outliers final: 1 residues processed: 216 average time/residue: 0.2579 time to fit residues: 73.5134 Evaluate side-chains 209 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9176 Z= 0.252 Angle : 0.643 9.911 12430 Z= 0.334 Chirality : 0.046 0.315 1365 Planarity : 0.005 0.070 1594 Dihedral : 7.920 110.141 1362 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.72 % Allowed : 8.70 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1158 helix: -1.22 (0.53), residues: 81 sheet: 0.00 (0.26), residues: 387 loop : -0.87 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 36 HIS 0.004 0.001 HIS D 56 PHE 0.016 0.001 PHE D 130 TYR 0.017 0.002 TYR F 82 ARG 0.004 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 212 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5359 (m-80) cc_final: 0.5104 (m-80) REVERT: A 641 ARG cc_start: 0.6563 (mpt90) cc_final: 0.6233 (mpt90) REVERT: A 797 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7502 (mtt90) REVERT: B 29 PHE cc_start: 0.7885 (t80) cc_final: 0.7577 (t80) REVERT: B 182 TYR cc_start: 0.7431 (m-80) cc_final: 0.7219 (m-80) REVERT: C 127 SER cc_start: 0.7789 (m) cc_final: 0.7313 (p) REVERT: C 185 ASP cc_start: 0.8355 (m-30) cc_final: 0.8077 (p0) REVERT: D 68 GLN cc_start: 0.7499 (mp10) cc_final: 0.7150 (mp10) REVERT: D 102 ASP cc_start: 0.7923 (t0) cc_final: 0.7613 (t0) REVERT: D 113 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7644 (mmmm) REVERT: D 131 GLU cc_start: 0.7129 (pp20) cc_final: 0.6876 (pp20) REVERT: D 136 ASP cc_start: 0.8112 (p0) cc_final: 0.7758 (p0) REVERT: D 268 GLU cc_start: 0.6766 (pp20) cc_final: 0.6347 (pp20) REVERT: D 317 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7344 (mp0) REVERT: D 332 TYR cc_start: 0.7209 (t80) cc_final: 0.6830 (t80) REVERT: F 11 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8096 (tp) REVERT: F 88 LEU cc_start: 0.8638 (mt) cc_final: 0.8394 (mt) outliers start: 17 outliers final: 11 residues processed: 213 average time/residue: 0.2441 time to fit residues: 69.1236 Evaluate side-chains 218 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 206 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9176 Z= 0.223 Angle : 0.612 7.475 12430 Z= 0.318 Chirality : 0.046 0.313 1365 Planarity : 0.005 0.064 1594 Dihedral : 7.719 109.093 1362 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.94 % Allowed : 11.13 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1158 helix: -1.20 (0.54), residues: 81 sheet: 0.03 (0.26), residues: 389 loop : -0.89 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.004 0.001 HIS D 56 PHE 0.015 0.001 PHE D 130 TYR 0.015 0.002 TYR F 97 ARG 0.003 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5376 (m-80) cc_final: 0.5123 (m-80) REVERT: A 641 ARG cc_start: 0.6552 (mpt90) cc_final: 0.6275 (mpt90) REVERT: B 29 PHE cc_start: 0.7887 (t80) cc_final: 0.7597 (t80) REVERT: B 182 TYR cc_start: 0.7458 (m-80) cc_final: 0.7221 (m-80) REVERT: C 127 SER cc_start: 0.7699 (m) cc_final: 0.7235 (p) REVERT: C 185 ASP cc_start: 0.8360 (m-30) cc_final: 0.8047 (p0) REVERT: D 102 ASP cc_start: 0.7937 (t0) cc_final: 0.7613 (t0) REVERT: D 113 LYS cc_start: 0.7964 (mmmt) cc_final: 0.7654 (mmmm) REVERT: D 131 GLU cc_start: 0.7095 (pp20) cc_final: 0.6865 (pp20) REVERT: D 136 ASP cc_start: 0.8115 (p0) cc_final: 0.7749 (p0) REVERT: D 192 LEU cc_start: 0.7738 (pp) cc_final: 0.7180 (pp) REVERT: D 268 GLU cc_start: 0.6795 (pp20) cc_final: 0.6376 (pp20) REVERT: D 332 TYR cc_start: 0.7224 (t80) cc_final: 0.6838 (t80) REVERT: F 52 LYS cc_start: 0.8004 (tttt) cc_final: 0.7273 (tttm) REVERT: F 88 LEU cc_start: 0.8623 (mt) cc_final: 0.7542 (mt) outliers start: 29 outliers final: 21 residues processed: 215 average time/residue: 0.2334 time to fit residues: 67.3786 Evaluate side-chains 223 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9176 Z= 0.251 Angle : 0.630 7.379 12430 Z= 0.327 Chirality : 0.046 0.311 1365 Planarity : 0.005 0.062 1594 Dihedral : 7.690 108.079 1362 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.14 % Allowed : 12.45 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1158 helix: -1.27 (0.53), residues: 81 sheet: 0.05 (0.27), residues: 388 loop : -0.94 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 36 HIS 0.004 0.001 HIS C 91 PHE 0.017 0.001 PHE D 130 TYR 0.017 0.002 TYR F 97 ARG 0.004 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 212 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5365 (m-80) cc_final: 0.5121 (m-80) REVERT: A 641 ARG cc_start: 0.6569 (mpt90) cc_final: 0.6284 (mpt90) REVERT: A 782 LYS cc_start: 0.7966 (ptpp) cc_final: 0.7472 (ptpp) REVERT: A 797 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7399 (mtt90) REVERT: B 29 PHE cc_start: 0.7909 (t80) cc_final: 0.7595 (t80) REVERT: C 11 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7430 (mp) REVERT: C 127 SER cc_start: 0.7716 (m) cc_final: 0.7247 (p) REVERT: C 185 ASP cc_start: 0.8348 (m-30) cc_final: 0.8048 (p0) REVERT: D 102 ASP cc_start: 0.7936 (t0) cc_final: 0.7652 (t0) REVERT: D 113 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7664 (mmmm) REVERT: D 131 GLU cc_start: 0.7105 (pp20) cc_final: 0.6877 (pp20) REVERT: D 136 ASP cc_start: 0.8121 (p0) cc_final: 0.7744 (p0) REVERT: D 268 GLU cc_start: 0.6840 (pp20) cc_final: 0.6393 (pp20) REVERT: D 325 MET cc_start: 0.7819 (tmm) cc_final: 0.7003 (tmm) REVERT: D 332 TYR cc_start: 0.7230 (t80) cc_final: 0.6846 (t80) REVERT: F 31 ASN cc_start: 0.7627 (m110) cc_final: 0.7392 (m110) REVERT: F 47 TRP cc_start: 0.7112 (t60) cc_final: 0.6700 (t60) outliers start: 31 outliers final: 22 residues processed: 221 average time/residue: 0.2387 time to fit residues: 70.3018 Evaluate side-chains 230 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 0.0020 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.0570 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9176 Z= 0.174 Angle : 0.594 11.309 12430 Z= 0.302 Chirality : 0.044 0.310 1365 Planarity : 0.005 0.064 1594 Dihedral : 7.363 107.059 1362 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.83 % Allowed : 14.27 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.24), residues: 1158 helix: -1.25 (0.52), residues: 82 sheet: 0.04 (0.27), residues: 384 loop : -0.86 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 36 HIS 0.002 0.001 HIS D 31 PHE 0.012 0.001 PHE C 209 TYR 0.011 0.001 TYR F 97 ARG 0.003 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5321 (m-80) cc_final: 0.5069 (m-80) REVERT: A 641 ARG cc_start: 0.6488 (mpt90) cc_final: 0.6195 (mpt90) REVERT: A 782 LYS cc_start: 0.7919 (ptpp) cc_final: 0.7552 (ptpp) REVERT: B 29 PHE cc_start: 0.7870 (t80) cc_final: 0.7557 (t80) REVERT: B 182 TYR cc_start: 0.7430 (m-80) cc_final: 0.7208 (m-80) REVERT: C 11 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7434 (mp) REVERT: C 127 SER cc_start: 0.7573 (m) cc_final: 0.7070 (p) REVERT: C 185 ASP cc_start: 0.8318 (m-30) cc_final: 0.8013 (p0) REVERT: D 102 ASP cc_start: 0.7917 (t0) cc_final: 0.7638 (t0) REVERT: D 113 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7675 (mmmm) REVERT: D 131 GLU cc_start: 0.7102 (pp20) cc_final: 0.6890 (pp20) REVERT: D 136 ASP cc_start: 0.8114 (p0) cc_final: 0.7723 (p0) REVERT: D 268 GLU cc_start: 0.6827 (pp20) cc_final: 0.6364 (pp20) REVERT: D 325 MET cc_start: 0.7758 (tmm) cc_final: 0.6781 (tmm) REVERT: D 332 TYR cc_start: 0.7213 (t80) cc_final: 0.6881 (t80) REVERT: E 60 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6793 (ttm170) REVERT: F 31 ASN cc_start: 0.7592 (m110) cc_final: 0.7344 (m110) REVERT: F 47 TRP cc_start: 0.7154 (t60) cc_final: 0.6780 (t60) outliers start: 28 outliers final: 18 residues processed: 221 average time/residue: 0.2343 time to fit residues: 69.0362 Evaluate side-chains 228 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 208 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN E 41 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9176 Z= 0.360 Angle : 0.694 10.095 12430 Z= 0.362 Chirality : 0.048 0.320 1365 Planarity : 0.005 0.065 1594 Dihedral : 7.879 107.369 1362 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.54 % Allowed : 14.37 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.11 (0.24), residues: 1158 helix: -1.56 (0.50), residues: 81 sheet: -0.02 (0.27), residues: 389 loop : -1.06 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 36 HIS 0.007 0.002 HIS C 91 PHE 0.022 0.002 PHE D 130 TYR 0.024 0.003 TYR F 97 ARG 0.007 0.001 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5453 (m-80) cc_final: 0.5211 (m-80) REVERT: A 641 ARG cc_start: 0.6631 (mpt90) cc_final: 0.6213 (mpt90) REVERT: A 779 THR cc_start: 0.6393 (OUTLIER) cc_final: 0.6094 (p) REVERT: A 782 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7645 (pttm) REVERT: B 29 PHE cc_start: 0.7879 (t80) cc_final: 0.7549 (t80) REVERT: C 11 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7481 (mp) REVERT: C 127 SER cc_start: 0.7811 (m) cc_final: 0.7331 (p) REVERT: C 185 ASP cc_start: 0.8389 (m-30) cc_final: 0.8002 (p0) REVERT: D 68 GLN cc_start: 0.7526 (mp10) cc_final: 0.7026 (mp10) REVERT: D 102 ASP cc_start: 0.7962 (t0) cc_final: 0.7685 (t0) REVERT: D 131 GLU cc_start: 0.7088 (pp20) cc_final: 0.6887 (pp20) REVERT: D 136 ASP cc_start: 0.8160 (p0) cc_final: 0.7797 (p0) REVERT: D 268 GLU cc_start: 0.6855 (pp20) cc_final: 0.6404 (pp20) REVERT: D 325 MET cc_start: 0.7965 (tmm) cc_final: 0.7163 (tmm) REVERT: D 332 TYR cc_start: 0.7272 (t80) cc_final: 0.6943 (t80) REVERT: E 28 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7689 (mmt90) REVERT: E 60 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6925 (ttm170) REVERT: F 31 ASN cc_start: 0.7677 (m110) cc_final: 0.7426 (m110) REVERT: F 47 TRP cc_start: 0.7093 (t60) cc_final: 0.6623 (t60) REVERT: F 52 LYS cc_start: 0.8245 (tppt) cc_final: 0.8021 (tppt) outliers start: 35 outliers final: 25 residues processed: 229 average time/residue: 0.2292 time to fit residues: 70.1525 Evaluate side-chains 245 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.0060 chunk 61 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9176 Z= 0.243 Angle : 0.651 9.474 12430 Z= 0.333 Chirality : 0.046 0.313 1365 Planarity : 0.005 0.066 1594 Dihedral : 7.693 107.196 1362 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.44 % Allowed : 15.28 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % 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: -1.10 (0.24), residues: 1158 helix: -1.38 (0.51), residues: 82 sheet: -0.02 (0.27), residues: 391 loop : -1.08 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.001 PHE D 130 TYR 0.016 0.002 TYR F 97 ARG 0.007 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5404 (m-80) cc_final: 0.5150 (m-80) REVERT: A 641 ARG cc_start: 0.6560 (mpt90) cc_final: 0.6233 (mpt90) REVERT: A 779 THR cc_start: 0.6372 (OUTLIER) cc_final: 0.6057 (p) REVERT: A 782 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7592 (pttm) REVERT: B 29 PHE cc_start: 0.7876 (t80) cc_final: 0.7532 (t80) REVERT: C 185 ASP cc_start: 0.8373 (m-30) cc_final: 0.7979 (p0) REVERT: D 102 ASP cc_start: 0.7922 (t0) cc_final: 0.7662 (t0) REVERT: D 136 ASP cc_start: 0.8152 (p0) cc_final: 0.7795 (p0) REVERT: D 268 GLU cc_start: 0.6932 (pp20) cc_final: 0.6477 (pp20) REVERT: D 332 TYR cc_start: 0.7228 (t80) cc_final: 0.6899 (t80) REVERT: E 28 ARG cc_start: 0.7960 (mmt90) cc_final: 0.7629 (mmt90) REVERT: E 60 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6860 (ttm170) REVERT: F 47 TRP cc_start: 0.7134 (t60) cc_final: 0.6740 (t60) outliers start: 34 outliers final: 26 residues processed: 230 average time/residue: 0.2302 time to fit residues: 70.8319 Evaluate side-chains 243 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 215 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9176 Z= 0.185 Angle : 0.633 10.334 12430 Z= 0.319 Chirality : 0.045 0.306 1365 Planarity : 0.005 0.066 1594 Dihedral : 7.353 105.014 1362 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.83 % Allowed : 15.69 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1158 helix: -1.08 (0.53), residues: 82 sheet: 0.07 (0.27), residues: 388 loop : -1.00 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 36 HIS 0.002 0.001 HIS D 31 PHE 0.012 0.001 PHE C 209 TYR 0.012 0.001 TYR C 173 ARG 0.005 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 220 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5373 (m-80) cc_final: 0.5110 (m-80) REVERT: A 641 ARG cc_start: 0.6472 (mpt90) cc_final: 0.6178 (mpt90) REVERT: A 779 THR cc_start: 0.6358 (OUTLIER) cc_final: 0.6066 (p) REVERT: A 782 LYS cc_start: 0.8004 (ptpp) cc_final: 0.7508 (pttm) REVERT: A 797 ARG cc_start: 0.7649 (mtt90) cc_final: 0.7408 (mtt90) REVERT: B 29 PHE cc_start: 0.7856 (t80) cc_final: 0.7516 (t80) REVERT: C 11 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7446 (mp) REVERT: C 185 ASP cc_start: 0.8348 (m-30) cc_final: 0.7973 (p0) REVERT: D 102 ASP cc_start: 0.7909 (t0) cc_final: 0.7640 (t0) REVERT: D 136 ASP cc_start: 0.8141 (p0) cc_final: 0.7774 (p0) REVERT: D 268 GLU cc_start: 0.6979 (pp20) cc_final: 0.6533 (pp20) REVERT: D 317 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7375 (mp0) REVERT: D 325 MET cc_start: 0.7646 (tmm) cc_final: 0.7269 (tmm) REVERT: D 332 TYR cc_start: 0.7217 (t80) cc_final: 0.6942 (t80) REVERT: E 28 ARG cc_start: 0.7925 (mmt90) cc_final: 0.6898 (mmt90) REVERT: E 60 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6703 (ttm170) REVERT: F 47 TRP cc_start: 0.7146 (t60) cc_final: 0.6869 (t60) REVERT: F 85 MET cc_start: 0.5706 (ppp) cc_final: 0.5342 (ppp) outliers start: 28 outliers final: 21 residues processed: 230 average time/residue: 0.2248 time to fit residues: 69.6022 Evaluate side-chains 243 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 93 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.0010 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 overall best weight: 0.7448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9176 Z= 0.243 Angle : 0.653 9.072 12430 Z= 0.332 Chirality : 0.046 0.314 1365 Planarity : 0.005 0.065 1594 Dihedral : 7.430 105.011 1362 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.64 % Allowed : 15.38 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.24), residues: 1158 helix: -1.02 (0.52), residues: 82 sheet: 0.07 (0.27), residues: 387 loop : -1.02 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 36 HIS 0.004 0.001 HIS C 91 PHE 0.016 0.001 PHE D 130 TYR 0.016 0.002 TYR F 97 ARG 0.006 0.000 ARG A 797 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5424 (m-80) cc_final: 0.5168 (m-80) REVERT: A 641 ARG cc_start: 0.6547 (mpt90) cc_final: 0.6243 (mpt90) REVERT: A 779 THR cc_start: 0.6395 (OUTLIER) cc_final: 0.6097 (p) REVERT: A 782 LYS cc_start: 0.8057 (ptpp) cc_final: 0.7580 (pttm) REVERT: B 29 PHE cc_start: 0.7876 (t80) cc_final: 0.7535 (t80) REVERT: C 11 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7497 (mp) REVERT: C 185 ASP cc_start: 0.8372 (m-30) cc_final: 0.7977 (p0) REVERT: D 102 ASP cc_start: 0.7931 (t0) cc_final: 0.7658 (t0) REVERT: D 136 ASP cc_start: 0.8153 (p0) cc_final: 0.7788 (p0) REVERT: D 325 MET cc_start: 0.7748 (tmm) cc_final: 0.7348 (tmm) REVERT: D 332 TYR cc_start: 0.7241 (t80) cc_final: 0.6968 (t80) REVERT: E 28 ARG cc_start: 0.7955 (mmt90) cc_final: 0.6917 (mmt90) REVERT: E 60 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6748 (ttm170) REVERT: F 47 TRP cc_start: 0.7118 (t60) cc_final: 0.6733 (t60) REVERT: F 85 MET cc_start: 0.5698 (ppp) cc_final: 0.5317 (ppp) outliers start: 36 outliers final: 30 residues processed: 228 average time/residue: 0.2257 time to fit residues: 68.7849 Evaluate side-chains 244 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.0020 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9176 Z= 0.212 Angle : 0.649 11.538 12430 Z= 0.327 Chirality : 0.046 0.312 1365 Planarity : 0.005 0.066 1594 Dihedral : 7.350 104.696 1362 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.34 % Allowed : 15.89 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1158 helix: -0.83 (0.52), residues: 82 sheet: 0.08 (0.27), residues: 388 loop : -1.02 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 36 HIS 0.003 0.001 HIS C 91 PHE 0.013 0.001 PHE D 130 TYR 0.014 0.002 TYR A 804 ARG 0.006 0.000 ARG A 797 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5409 (m-80) cc_final: 0.5145 (m-80) REVERT: A 641 ARG cc_start: 0.6529 (mpt90) cc_final: 0.6230 (mpt90) REVERT: A 779 THR cc_start: 0.6386 (OUTLIER) cc_final: 0.6082 (p) REVERT: A 782 LYS cc_start: 0.8042 (ptpp) cc_final: 0.7559 (pttm) REVERT: A 797 ARG cc_start: 0.7716 (mtt90) cc_final: 0.7473 (mtt90) REVERT: B 29 PHE cc_start: 0.7869 (t80) cc_final: 0.7529 (t80) REVERT: C 11 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7465 (mp) REVERT: C 185 ASP cc_start: 0.8353 (m-30) cc_final: 0.7963 (p0) REVERT: D 102 ASP cc_start: 0.7919 (t0) cc_final: 0.7652 (t0) REVERT: D 136 ASP cc_start: 0.8152 (p0) cc_final: 0.7800 (p0) REVERT: D 231 ASP cc_start: 0.7749 (t0) cc_final: 0.7423 (t0) REVERT: D 332 TYR cc_start: 0.7222 (t80) cc_final: 0.6949 (t80) REVERT: E 28 ARG cc_start: 0.7931 (mmt90) cc_final: 0.6892 (mmt90) REVERT: E 60 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6690 (ttm170) REVERT: F 47 TRP cc_start: 0.7139 (t60) cc_final: 0.6776 (t60) REVERT: F 85 MET cc_start: 0.5738 (ppp) cc_final: 0.5331 (ppp) REVERT: F 86 ASN cc_start: 0.7586 (m110) cc_final: 0.7354 (m-40) outliers start: 33 outliers final: 29 residues processed: 225 average time/residue: 0.2285 time to fit residues: 68.8110 Evaluate side-chains 243 residues out of total 988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain B residue 106 PHE Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 190 LYS Chi-restraints excluded: chain C residue 194 CYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain F residue 93 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 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 = 0.4294 r_free = 0.4294 target = 0.172315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.146578 restraints weight = 15205.319| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.26 r_work: 0.3840 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9176 Z= 0.195 Angle : 0.633 10.772 12430 Z= 0.318 Chirality : 0.045 0.308 1365 Planarity : 0.005 0.065 1594 Dihedral : 7.156 103.438 1362 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.24 % Allowed : 15.89 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1158 helix: -0.63 (0.53), residues: 82 sheet: 0.17 (0.27), residues: 394 loop : -1.00 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 36 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE C 209 TYR 0.015 0.001 TYR C 173 ARG 0.007 0.000 ARG A 797 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2544.05 seconds wall clock time: 45 minutes 55.14 seconds (2755.14 seconds total)