Starting phenix.real_space_refine on Sat May 17 21:55:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqw_37756/05_2025/8wqw_37756.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqw_37756/05_2025/8wqw_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/cci-nas-00/data/ceres_data/8wqw_37756/05_2025/8wqw_37756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqw_37756/05_2025/8wqw_37756.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqw_37756/05_2025/8wqw_37756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqw_37756/05_2025/8wqw_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. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.03, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 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: 1.28 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: 2.93 Time building geometry restraints manager: 2.76 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: 0.00 - 3.53: 12373 3.53 - 7.06: 52 7.06 - 10.59: 3 10.59 - 14.12: 1 14.12 - 17.65: 1 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 3.040 nonbonded pdb=" O HIS C 189 " pdb=" NH2 ARG C 211 " model vdw 2.174 3.120 nonbonded pdb=" NH2 ARG B 98 " pdb=" OD2 ASP B 107 " model vdw 2.207 3.120 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER C 208 " model vdw 2.258 3.120 nonbonded pdb=" NE2 HIS D 243 " pdb=" OH TYR D 332 " model vdw 2.265 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 10.710 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: 23.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- 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 9204 Z= 0.195 Angle : 0.717 17.651 12491 Z= 0.382 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00929 ( 2) link_NAG-ASN : angle 5.23168 ( 6) link_ALPHA1-4 : bond 0.01241 ( 1) link_ALPHA1-4 : angle 4.54957 ( 3) link_BETA1-4 : bond 0.00995 ( 2) link_BETA1-4 : angle 1.93743 ( 6) hydrogen bonds : bond 0.16457 ( 272) hydrogen bonds : angle 7.65334 ( 729) SS BOND : bond 0.00652 ( 23) SS BOND : angle 1.37869 ( 46) covalent geometry : bond 0.00495 ( 9176) covalent geometry : angle 0.69990 (12430) *********************** 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 to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.936 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: 0.2481 time to fit residues: 70.3965 Evaluate side-chains 209 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 0.5980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN F 84 GLN F 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.171871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.144730 restraints weight = 15481.542| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.56 r_work: 0.3810 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9204 Z= 0.152 Angle : 0.654 9.715 12491 Z= 0.335 Chirality : 0.045 0.309 1365 Planarity : 0.005 0.070 1594 Dihedral : 7.951 113.076 1362 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.21 % Allowed : 8.40 % Favored : 90.38 % 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: -0.87 (0.24), residues: 1158 helix: -1.13 (0.53), residues: 81 sheet: -0.00 (0.26), residues: 389 loop : -0.83 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 36 HIS 0.003 0.001 HIS C 91 PHE 0.014 0.001 PHE D 130 TYR 0.017 0.002 TYR F 82 ARG 0.004 0.000 ARG A 797 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 2) link_NAG-ASN : angle 4.53499 ( 6) link_ALPHA1-4 : bond 0.02120 ( 1) link_ALPHA1-4 : angle 4.67167 ( 3) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 1.55586 ( 6) hydrogen bonds : bond 0.04147 ( 272) hydrogen bonds : angle 6.33481 ( 729) SS BOND : bond 0.00632 ( 23) SS BOND : angle 1.38799 ( 46) covalent geometry : bond 0.00340 ( 9176) covalent geometry : angle 0.63730 (12430) *********************** 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 232 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5647 (m-80) cc_final: 0.5309 (m-80) REVERT: A 641 ARG cc_start: 0.6800 (mpt90) cc_final: 0.6526 (mpt90) REVERT: A 797 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7775 (mtt90) REVERT: B 29 PHE cc_start: 0.8062 (t80) cc_final: 0.7778 (t80) REVERT: B 182 TYR cc_start: 0.7896 (m-80) cc_final: 0.7686 (m-80) REVERT: C 127 SER cc_start: 0.7863 (m) cc_final: 0.7413 (p) REVERT: C 185 ASP cc_start: 0.8602 (m-30) cc_final: 0.8108 (p0) REVERT: D 68 GLN cc_start: 0.7549 (mp10) cc_final: 0.7305 (mp10) REVERT: D 102 ASP cc_start: 0.8206 (t0) cc_final: 0.7886 (t0) REVERT: D 113 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7861 (mmmm) REVERT: D 131 GLU cc_start: 0.7711 (pp20) cc_final: 0.7464 (pp20) REVERT: D 136 ASP cc_start: 0.8485 (p0) cc_final: 0.8129 (p0) REVERT: D 268 GLU cc_start: 0.6975 (pp20) cc_final: 0.6513 (pp20) REVERT: D 270 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7831 (mt-10) REVERT: D 317 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7404 (mp0) REVERT: D 332 TYR cc_start: 0.7798 (t80) cc_final: 0.7399 (t80) REVERT: F 88 LEU cc_start: 0.8587 (mt) cc_final: 0.8247 (mt) outliers start: 12 outliers final: 10 residues processed: 222 average time/residue: 0.2285 time to fit residues: 67.2205 Evaluate side-chains 226 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 11 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 104 LYS 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 62 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 88 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN C 152 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.170700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.143946 restraints weight = 15751.413| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.43 r_work: 0.3810 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9204 Z= 0.184 Angle : 0.662 8.241 12491 Z= 0.342 Chirality : 0.046 0.311 1365 Planarity : 0.005 0.064 1594 Dihedral : 7.883 110.782 1362 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.33 % Allowed : 10.83 % Favored : 86.84 % 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: -0.98 (0.24), residues: 1158 helix: -1.22 (0.53), residues: 82 sheet: -0.02 (0.26), residues: 390 loop : -0.94 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 36 HIS 0.004 0.001 HIS C 91 PHE 0.016 0.001 PHE D 130 TYR 0.018 0.002 TYR F 97 ARG 0.004 0.000 ARG D 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00881 ( 2) link_NAG-ASN : angle 4.51066 ( 6) link_ALPHA1-4 : bond 0.02082 ( 1) link_ALPHA1-4 : angle 4.84341 ( 3) link_BETA1-4 : bond 0.00590 ( 2) link_BETA1-4 : angle 1.81885 ( 6) hydrogen bonds : bond 0.03945 ( 272) hydrogen bonds : angle 6.18694 ( 729) SS BOND : bond 0.00673 ( 23) SS BOND : angle 1.63613 ( 46) covalent geometry : bond 0.00409 ( 9176) covalent geometry : angle 0.64275 (12430) *********************** 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 237 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5643 (m-80) cc_final: 0.5334 (m-80) REVERT: A 641 ARG cc_start: 0.6925 (mpt90) cc_final: 0.6655 (mpt90) REVERT: B 29 PHE cc_start: 0.8087 (t80) cc_final: 0.7846 (t80) REVERT: C 127 SER cc_start: 0.7915 (m) cc_final: 0.7460 (p) REVERT: C 185 ASP cc_start: 0.8527 (m-30) cc_final: 0.8096 (p0) REVERT: D 102 ASP cc_start: 0.8162 (t0) cc_final: 0.7855 (t0) REVERT: D 113 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7846 (mmmm) REVERT: D 131 GLU cc_start: 0.7664 (pp20) cc_final: 0.7455 (pp20) REVERT: D 136 ASP cc_start: 0.8420 (p0) cc_final: 0.8040 (p0) REVERT: D 192 LEU cc_start: 0.7813 (pp) cc_final: 0.7276 (pp) REVERT: D 268 GLU cc_start: 0.6983 (pp20) cc_final: 0.6554 (pp20) REVERT: D 332 TYR cc_start: 0.7774 (t80) cc_final: 0.7369 (t80) REVERT: F 88 LEU cc_start: 0.8665 (mt) cc_final: 0.8458 (mt) outliers start: 23 outliers final: 17 residues processed: 221 average time/residue: 0.2324 time to fit residues: 68.3665 Evaluate side-chains 226 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 89 LEU Chi-restraints excluded: chain C residue 179 LEU 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 341 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.171336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144927 restraints weight = 15418.482| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.46 r_work: 0.3817 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9204 Z= 0.147 Angle : 0.650 8.280 12491 Z= 0.332 Chirality : 0.045 0.306 1365 Planarity : 0.005 0.063 1594 Dihedral : 7.696 109.252 1362 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.53 % Allowed : 12.85 % Favored : 84.62 % 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: -1.00 (0.24), residues: 1158 helix: -1.22 (0.52), residues: 82 sheet: -0.01 (0.26), residues: 386 loop : -0.97 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.003 0.001 HIS C 91 PHE 0.014 0.001 PHE D 130 TYR 0.017 0.002 TYR F 82 ARG 0.005 0.000 ARG A 797 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 2) link_NAG-ASN : angle 4.43605 ( 6) link_ALPHA1-4 : bond 0.01941 ( 1) link_ALPHA1-4 : angle 4.60767 ( 3) link_BETA1-4 : bond 0.00564 ( 2) link_BETA1-4 : angle 1.69204 ( 6) hydrogen bonds : bond 0.03518 ( 272) hydrogen bonds : angle 5.94469 ( 729) SS BOND : bond 0.00679 ( 23) SS BOND : angle 1.58062 ( 46) covalent geometry : bond 0.00332 ( 9176) covalent geometry : angle 0.63148 (12430) *********************** 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 237 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5623 (m-80) cc_final: 0.5330 (m-80) REVERT: A 641 ARG cc_start: 0.6839 (mpt90) cc_final: 0.6520 (mpt90) REVERT: B 29 PHE cc_start: 0.8125 (t80) cc_final: 0.7869 (t80) REVERT: C 127 SER cc_start: 0.7828 (m) cc_final: 0.7366 (p) REVERT: C 152 ASN cc_start: 0.7196 (p0) cc_final: 0.6678 (p0) REVERT: C 185 ASP cc_start: 0.8561 (m-30) cc_final: 0.8077 (p0) REVERT: C 187 GLU cc_start: 0.7340 (mp0) cc_final: 0.7073 (mp0) REVERT: D 68 GLN cc_start: 0.7564 (mp10) cc_final: 0.7209 (mp10) REVERT: D 102 ASP cc_start: 0.8171 (t0) cc_final: 0.7882 (t0) REVERT: D 113 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7819 (mmmm) REVERT: D 131 GLU cc_start: 0.7725 (pp20) cc_final: 0.7517 (pp20) REVERT: D 136 ASP cc_start: 0.8463 (p0) cc_final: 0.8076 (p0) REVERT: D 268 GLU cc_start: 0.7056 (pp20) cc_final: 0.6553 (pp20) REVERT: D 325 MET cc_start: 0.8136 (tmm) cc_final: 0.7198 (tmm) REVERT: D 332 TYR cc_start: 0.7779 (t80) cc_final: 0.7413 (t80) REVERT: E 28 ARG cc_start: 0.8302 (mmt90) cc_final: 0.8100 (mmt90) REVERT: F 47 TRP cc_start: 0.7480 (t60) cc_final: 0.7150 (t60) outliers start: 25 outliers final: 18 residues processed: 219 average time/residue: 0.2350 time to fit residues: 68.5220 Evaluate side-chains 225 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 341 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 44 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.0770 chunk 98 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4289 r_free = 0.4289 target = 0.171909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.145450 restraints weight = 15365.639| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.50 r_work: 0.3831 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9204 Z= 0.121 Angle : 0.615 10.949 12491 Z= 0.312 Chirality : 0.045 0.306 1365 Planarity : 0.005 0.063 1594 Dihedral : 7.430 108.493 1362 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.23 % Allowed : 14.68 % Favored : 83.10 % 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: -1.16 (0.52), residues: 83 sheet: 0.02 (0.27), residues: 376 loop : -0.92 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 36 HIS 0.002 0.001 HIS C 91 PHE 0.012 0.001 PHE C 209 TYR 0.011 0.001 TYR F 97 ARG 0.006 0.000 ARG A 797 Details of bonding type rmsd link_NAG-ASN : bond 0.00799 ( 2) link_NAG-ASN : angle 4.31385 ( 6) link_ALPHA1-4 : bond 0.02105 ( 1) link_ALPHA1-4 : angle 4.36154 ( 3) link_BETA1-4 : bond 0.00551 ( 2) link_BETA1-4 : angle 1.52082 ( 6) hydrogen bonds : bond 0.03251 ( 272) hydrogen bonds : angle 5.60367 ( 729) SS BOND : bond 0.00624 ( 23) SS BOND : angle 1.29203 ( 46) covalent geometry : bond 0.00271 ( 9176) covalent geometry : angle 0.59898 (12430) *********************** 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 235 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5663 (m-80) cc_final: 0.5372 (m-80) REVERT: A 641 ARG cc_start: 0.6803 (mpt90) cc_final: 0.6395 (mpt90) REVERT: B 29 PHE cc_start: 0.8105 (t80) cc_final: 0.7850 (t80) REVERT: B 182 TYR cc_start: 0.7871 (m-80) cc_final: 0.7648 (m-80) REVERT: C 11 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7608 (mp) REVERT: C 127 SER cc_start: 0.7683 (m) cc_final: 0.7198 (p) REVERT: C 152 ASN cc_start: 0.7291 (p0) cc_final: 0.6794 (p0) REVERT: C 185 ASP cc_start: 0.8561 (m-30) cc_final: 0.8054 (p0) REVERT: C 187 GLU cc_start: 0.7258 (mp0) cc_final: 0.6926 (mp0) REVERT: D 68 GLN cc_start: 0.7561 (mp10) cc_final: 0.7190 (mp10) REVERT: D 102 ASP cc_start: 0.8209 (t0) cc_final: 0.7930 (t0) REVERT: D 113 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7813 (mmmm) REVERT: D 136 ASP cc_start: 0.8456 (p0) cc_final: 0.8071 (p0) REVERT: D 268 GLU cc_start: 0.7031 (pp20) cc_final: 0.6517 (pp20) REVERT: D 332 TYR cc_start: 0.7790 (t80) cc_final: 0.7414 (t80) REVERT: E 26 SER cc_start: 0.8146 (t) cc_final: 0.7943 (t) REVERT: F 47 TRP cc_start: 0.7490 (t60) cc_final: 0.7208 (t60) REVERT: F 88 LEU cc_start: 0.8678 (mt) cc_final: 0.8353 (mt) outliers start: 22 outliers final: 15 residues processed: 220 average time/residue: 0.2334 time to fit residues: 68.7368 Evaluate side-chains 226 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain D residue 49 CYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 284 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 82 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: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4277 r_free = 0.4277 target = 0.171236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.144167 restraints weight = 15542.590| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.54 r_work: 0.3804 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9204 Z= 0.165 Angle : 0.648 9.666 12491 Z= 0.329 Chirality : 0.045 0.308 1365 Planarity : 0.005 0.064 1594 Dihedral : 7.511 107.585 1362 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.94 % Allowed : 13.77 % Favored : 83.30 % 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: -1.16 (0.51), residues: 82 sheet: 0.06 (0.27), residues: 388 loop : -0.99 (0.23), residues: 688 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 0.017 0.002 TYR F 97 ARG 0.010 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00812 ( 2) link_NAG-ASN : angle 4.28545 ( 6) link_ALPHA1-4 : bond 0.01841 ( 1) link_ALPHA1-4 : angle 4.56730 ( 3) link_BETA1-4 : bond 0.00521 ( 2) link_BETA1-4 : angle 1.75392 ( 6) hydrogen bonds : bond 0.03443 ( 272) hydrogen bonds : angle 5.68469 ( 729) SS BOND : bond 0.00654 ( 23) SS BOND : angle 1.50109 ( 46) covalent geometry : bond 0.00374 ( 9176) covalent geometry : angle 0.63092 (12430) *********************** 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 241 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5753 (m-80) cc_final: 0.5449 (m-80) REVERT: A 641 ARG cc_start: 0.6867 (mpt90) cc_final: 0.6502 (mpt90) REVERT: B 29 PHE cc_start: 0.8090 (t80) cc_final: 0.7823 (t80) REVERT: C 152 ASN cc_start: 0.7396 (p0) cc_final: 0.6962 (p0) REVERT: C 185 ASP cc_start: 0.8566 (m-30) cc_final: 0.8063 (p0) REVERT: C 187 GLU cc_start: 0.7311 (mp0) cc_final: 0.6954 (mp0) REVERT: D 68 GLN cc_start: 0.7540 (mp10) cc_final: 0.7178 (mp10) REVERT: D 102 ASP cc_start: 0.8236 (t0) cc_final: 0.7953 (t0) REVERT: D 113 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7817 (mmmm) REVERT: D 136 ASP cc_start: 0.8421 (p0) cc_final: 0.8034 (p0) REVERT: D 268 GLU cc_start: 0.7063 (pp20) cc_final: 0.6546 (pp20) REVERT: D 325 MET cc_start: 0.8128 (tmm) cc_final: 0.7562 (tmm) REVERT: D 332 TYR cc_start: 0.7771 (t80) cc_final: 0.7417 (t80) REVERT: F 47 TRP cc_start: 0.7504 (t60) cc_final: 0.7241 (t60) outliers start: 29 outliers final: 22 residues processed: 222 average time/residue: 0.2333 time to fit residues: 69.2273 Evaluate side-chains 230 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 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 190 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 7 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 96 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4281 r_free = 0.4281 target = 0.171601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.145318 restraints weight = 15718.894| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.37 r_work: 0.3819 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9204 Z= 0.153 Angle : 0.640 9.193 12491 Z= 0.325 Chirality : 0.045 0.311 1365 Planarity : 0.005 0.065 1594 Dihedral : 7.490 106.875 1362 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.83 % Allowed : 14.68 % Favored : 82.49 % 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: -1.02 (0.51), residues: 82 sheet: 0.06 (0.26), residues: 395 loop : -1.01 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 36 HIS 0.004 0.001 HIS C 91 PHE 0.014 0.001 PHE D 130 TYR 0.015 0.002 TYR F 97 ARG 0.008 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00806 ( 2) link_NAG-ASN : angle 4.31826 ( 6) link_ALPHA1-4 : bond 0.01910 ( 1) link_ALPHA1-4 : angle 4.47594 ( 3) link_BETA1-4 : bond 0.00556 ( 2) link_BETA1-4 : angle 1.64063 ( 6) hydrogen bonds : bond 0.03325 ( 272) hydrogen bonds : angle 5.61914 ( 729) SS BOND : bond 0.00657 ( 23) SS BOND : angle 1.47325 ( 46) covalent geometry : bond 0.00345 ( 9176) covalent geometry : angle 0.62369 (12430) *********************** 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 240 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5728 (m-80) cc_final: 0.5445 (m-80) REVERT: A 641 ARG cc_start: 0.6857 (mpt90) cc_final: 0.6512 (mpt90) REVERT: A 779 THR cc_start: 0.6486 (OUTLIER) cc_final: 0.6194 (p) REVERT: A 782 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7308 (ptpp) REVERT: B 29 PHE cc_start: 0.8078 (t80) cc_final: 0.7786 (t80) REVERT: C 152 ASN cc_start: 0.7365 (p0) cc_final: 0.6954 (p0) REVERT: C 185 ASP cc_start: 0.8547 (m-30) cc_final: 0.8083 (p0) REVERT: C 187 GLU cc_start: 0.7276 (mp0) cc_final: 0.6949 (mp0) REVERT: D 68 GLN cc_start: 0.7547 (mp10) cc_final: 0.7232 (mp10) REVERT: D 102 ASP cc_start: 0.8161 (t0) cc_final: 0.7882 (t0) REVERT: D 113 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7831 (mmmm) REVERT: D 136 ASP cc_start: 0.8389 (p0) cc_final: 0.7968 (p0) REVERT: D 268 GLU cc_start: 0.7061 (pp20) cc_final: 0.6562 (pp20) REVERT: D 317 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7527 (mp0) REVERT: D 332 TYR cc_start: 0.7760 (t80) cc_final: 0.7419 (t80) REVERT: F 85 MET cc_start: 0.6112 (ptp) cc_final: 0.5645 (ptp) REVERT: F 88 LEU cc_start: 0.8682 (mt) cc_final: 0.8180 (mt) outliers start: 28 outliers final: 23 residues processed: 222 average time/residue: 0.2377 time to fit residues: 70.1347 Evaluate side-chains 234 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 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 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 131 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 62 SER 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 61 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4261 r_free = 0.4261 target = 0.169692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.143533 restraints weight = 15639.377| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.36 r_work: 0.3813 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9204 Z= 0.196 Angle : 0.684 8.746 12491 Z= 0.349 Chirality : 0.047 0.310 1365 Planarity : 0.005 0.064 1594 Dihedral : 7.657 106.477 1362 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.54 % Allowed : 14.57 % Favored : 81.88 % 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: -1.00 (0.24), residues: 1158 helix: -1.07 (0.51), residues: 82 sheet: 0.10 (0.26), residues: 396 loop : -1.08 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 47 HIS 0.005 0.001 HIS C 91 PHE 0.018 0.002 PHE D 130 TYR 0.019 0.002 TYR F 97 ARG 0.008 0.001 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 2) link_NAG-ASN : angle 4.33693 ( 6) link_ALPHA1-4 : bond 0.01932 ( 1) link_ALPHA1-4 : angle 4.81072 ( 3) link_BETA1-4 : bond 0.00637 ( 2) link_BETA1-4 : angle 1.82566 ( 6) hydrogen bonds : bond 0.03698 ( 272) hydrogen bonds : angle 5.84767 ( 729) SS BOND : bond 0.00761 ( 23) SS BOND : angle 1.75954 ( 46) covalent geometry : bond 0.00440 ( 9176) covalent geometry : angle 0.66517 (12430) *********************** 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 247 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5738 (m-80) cc_final: 0.5433 (m-80) REVERT: A 641 ARG cc_start: 0.6936 (mpt90) cc_final: 0.6622 (mpt90) REVERT: A 779 THR cc_start: 0.6610 (OUTLIER) cc_final: 0.6293 (p) REVERT: A 782 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7402 (ptpp) REVERT: B 29 PHE cc_start: 0.8096 (t80) cc_final: 0.7805 (t80) REVERT: C 152 ASN cc_start: 0.7457 (p0) cc_final: 0.7079 (p0) REVERT: C 185 ASP cc_start: 0.8559 (m-30) cc_final: 0.8070 (p0) REVERT: C 187 GLU cc_start: 0.7350 (mp0) cc_final: 0.7004 (mp0) REVERT: D 68 GLN cc_start: 0.7551 (mp10) cc_final: 0.7220 (mp10) REVERT: D 102 ASP cc_start: 0.8173 (t0) cc_final: 0.7901 (t0) REVERT: D 113 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7825 (mmmm) REVERT: D 136 ASP cc_start: 0.8444 (p0) cc_final: 0.8021 (p0) REVERT: D 268 GLU cc_start: 0.7013 (pp20) cc_final: 0.6544 (pp20) REVERT: D 332 TYR cc_start: 0.7789 (t80) cc_final: 0.7460 (t80) REVERT: F 31 ASN cc_start: 0.7915 (m110) cc_final: 0.7661 (m110) REVERT: F 52 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8183 (ttmm) REVERT: F 85 MET cc_start: 0.6112 (ptp) cc_final: 0.5656 (ptp) REVERT: F 88 LEU cc_start: 0.8705 (mt) cc_final: 0.8195 (mt) outliers start: 35 outliers final: 30 residues processed: 225 average time/residue: 0.2574 time to fit residues: 77.0925 Evaluate side-chains 242 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 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 190 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 74 ILE 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 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4267 r_free = 0.4267 target = 0.170290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.143754 restraints weight = 15422.697| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.51 r_work: 0.3810 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9204 Z= 0.166 Angle : 0.664 8.618 12491 Z= 0.337 Chirality : 0.046 0.311 1365 Planarity : 0.005 0.065 1594 Dihedral : 7.571 105.913 1362 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.34 % Allowed : 14.98 % Favored : 81.68 % 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: -0.99 (0.24), residues: 1158 helix: -1.00 (0.51), residues: 82 sheet: 0.09 (0.26), residues: 392 loop : -1.06 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 47 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.001 PHE C 209 TYR 0.017 0.002 TYR F 97 ARG 0.008 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 2) link_NAG-ASN : angle 4.35438 ( 6) link_ALPHA1-4 : bond 0.01914 ( 1) link_ALPHA1-4 : angle 4.60776 ( 3) link_BETA1-4 : bond 0.00614 ( 2) link_BETA1-4 : angle 1.66992 ( 6) hydrogen bonds : bond 0.03386 ( 272) hydrogen bonds : angle 5.73348 ( 729) SS BOND : bond 0.00705 ( 23) SS BOND : angle 1.57764 ( 46) covalent geometry : bond 0.00373 ( 9176) covalent geometry : angle 0.64630 (12430) *********************** 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 244 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5742 (m-80) cc_final: 0.5427 (m-80) REVERT: A 641 ARG cc_start: 0.6911 (mpt90) cc_final: 0.6574 (mpt90) REVERT: A 779 THR cc_start: 0.6634 (OUTLIER) cc_final: 0.6301 (p) REVERT: A 782 LYS cc_start: 0.7987 (ptpp) cc_final: 0.7401 (ptpp) REVERT: B 29 PHE cc_start: 0.8091 (t80) cc_final: 0.7811 (t80) REVERT: C 152 ASN cc_start: 0.7479 (p0) cc_final: 0.7096 (p0) REVERT: C 185 ASP cc_start: 0.8596 (m-30) cc_final: 0.8046 (p0) REVERT: C 187 GLU cc_start: 0.7290 (mp0) cc_final: 0.6934 (mp0) REVERT: D 68 GLN cc_start: 0.7566 (mp10) cc_final: 0.7230 (mp10) REVERT: D 102 ASP cc_start: 0.8208 (t0) cc_final: 0.7945 (t0) REVERT: D 113 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7808 (mmmm) REVERT: D 136 ASP cc_start: 0.8449 (p0) cc_final: 0.8030 (p0) REVERT: D 243 HIS cc_start: 0.8036 (p-80) cc_final: 0.7628 (p90) REVERT: D 268 GLU cc_start: 0.7238 (pp20) cc_final: 0.6741 (pp20) REVERT: D 317 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7486 (mp0) REVERT: D 332 TYR cc_start: 0.7806 (t80) cc_final: 0.7484 (t80) REVERT: F 31 ASN cc_start: 0.7873 (m110) cc_final: 0.7619 (m110) REVERT: F 62 TYR cc_start: 0.8116 (m-80) cc_final: 0.7845 (m-80) REVERT: F 85 MET cc_start: 0.6151 (ptp) cc_final: 0.5646 (ptp) REVERT: F 88 LEU cc_start: 0.8677 (mt) cc_final: 0.8159 (mt) outliers start: 33 outliers final: 31 residues processed: 223 average time/residue: 0.2536 time to fit residues: 75.6943 Evaluate side-chains 243 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 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 131 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 74 ILE 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 61 ASP Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 113 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 112 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4283 r_free = 0.4283 target = 0.171799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.145972 restraints weight = 15394.874| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.35 r_work: 0.3823 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9204 Z= 0.137 Angle : 0.652 8.714 12491 Z= 0.329 Chirality : 0.045 0.305 1365 Planarity : 0.005 0.065 1594 Dihedral : 7.426 104.926 1362 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.94 % Allowed : 15.59 % 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: -1.01 (0.24), residues: 1158 helix: -0.87 (0.52), residues: 83 sheet: 0.05 (0.26), residues: 392 loop : -1.08 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 47 HIS 0.003 0.001 HIS C 91 PHE 0.014 0.001 PHE C 209 TYR 0.015 0.002 TYR C 173 ARG 0.008 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00792 ( 2) link_NAG-ASN : angle 4.26275 ( 6) link_ALPHA1-4 : bond 0.01883 ( 1) link_ALPHA1-4 : angle 4.39132 ( 3) link_BETA1-4 : bond 0.00535 ( 2) link_BETA1-4 : angle 1.51314 ( 6) hydrogen bonds : bond 0.03134 ( 272) hydrogen bonds : angle 5.57045 ( 729) SS BOND : bond 0.00637 ( 23) SS BOND : angle 1.54195 ( 46) covalent geometry : bond 0.00309 ( 9176) covalent geometry : angle 0.63590 (12430) ********************** 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 240 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 PHE cc_start: 0.5716 (m-80) cc_final: 0.5414 (m-80) REVERT: A 641 ARG cc_start: 0.6808 (mpt90) cc_final: 0.6469 (mpt90) REVERT: A 779 THR cc_start: 0.6605 (OUTLIER) cc_final: 0.6282 (p) REVERT: A 782 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7343 (ptpp) REVERT: B 29 PHE cc_start: 0.8084 (t80) cc_final: 0.7803 (t80) REVERT: C 152 ASN cc_start: 0.7423 (p0) cc_final: 0.7035 (p0) REVERT: C 185 ASP cc_start: 0.8581 (m-30) cc_final: 0.8069 (p0) REVERT: C 187 GLU cc_start: 0.7237 (mp0) cc_final: 0.6903 (mp0) REVERT: D 68 GLN cc_start: 0.7560 (mp10) cc_final: 0.7277 (mp10) REVERT: D 102 ASP cc_start: 0.8067 (t0) cc_final: 0.7803 (t0) REVERT: D 113 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7815 (mmmm) REVERT: D 136 ASP cc_start: 0.8433 (p0) cc_final: 0.7985 (p0) REVERT: D 268 GLU cc_start: 0.7217 (pp20) cc_final: 0.6759 (pp20) REVERT: D 332 TYR cc_start: 0.7763 (t80) cc_final: 0.7484 (t80) REVERT: F 31 ASN cc_start: 0.7866 (m110) cc_final: 0.7638 (m110) REVERT: F 52 LYS cc_start: 0.8393 (ttmm) cc_final: 0.8086 (ttmm) REVERT: F 62 TYR cc_start: 0.8109 (m-80) cc_final: 0.7883 (m-80) REVERT: F 85 MET cc_start: 0.6091 (ptp) cc_final: 0.5644 (ptp) REVERT: F 88 LEU cc_start: 0.8711 (mt) cc_final: 0.8196 (mt) outliers start: 29 outliers final: 28 residues processed: 223 average time/residue: 0.2346 time to fit residues: 69.8196 Evaluate side-chains 236 residues out of total 988 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 131 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 74 ILE 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 61 ASP Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.8980 chunk 106 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 20 optimal weight: 0.0970 chunk 112 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.173556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147894 restraints weight = 15472.586| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.36 r_work: 0.3861 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9204 Z= 0.105 Angle : 0.619 8.744 12491 Z= 0.310 Chirality : 0.044 0.299 1365 Planarity : 0.005 0.066 1594 Dihedral : 7.074 103.534 1362 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.23 % Allowed : 16.60 % Favored : 81.17 % 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: -0.58 (0.53), residues: 83 sheet: 0.14 (0.27), residues: 389 loop : -0.99 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 47 HIS 0.002 0.001 HIS D 31 PHE 0.012 0.001 PHE C 209 TYR 0.017 0.001 TYR C 173 ARG 0.008 0.000 ARG E 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 2) link_NAG-ASN : angle 4.16355 ( 6) link_ALPHA1-4 : bond 0.01798 ( 1) link_ALPHA1-4 : angle 3.93869 ( 3) link_BETA1-4 : bond 0.00444 ( 2) link_BETA1-4 : angle 1.24649 ( 6) hydrogen bonds : bond 0.02791 ( 272) hydrogen bonds : angle 5.23673 ( 729) SS BOND : bond 0.00448 ( 23) SS BOND : angle 1.29409 ( 46) covalent geometry : bond 0.00242 ( 9176) covalent geometry : angle 0.60490 (12430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.20 seconds wall clock time: 86 minutes 51.98 seconds (5211.98 seconds total)