Starting phenix.real_space_refine on Thu Dec 26 10:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z16_14442/12_2024/7z16_14442_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z16_14442/12_2024/7z16_14442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z16_14442/12_2024/7z16_14442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z16_14442/12_2024/7z16_14442.map" model { file = "/net/cci-nas-00/data/ceres_data/7z16_14442/12_2024/7z16_14442_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z16_14442/12_2024/7z16_14442_neut_trim.cif" } resolution = 2.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 14074 2.51 5 N 4006 2.21 5 O 4260 1.98 5 H 22240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44690 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "E" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "I" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3899 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3899 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "L" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14336 SG CYS D 241 40.982 105.150 105.378 1.00 23.38 S ATOM 14375 SG CYS D 244 42.954 108.356 104.773 1.00 24.42 S ATOM 14695 SG CYS D 266 44.401 105.071 103.784 1.00 20.80 S ATOM 14775 SG CYS D 272 43.856 105.870 107.579 1.00 23.09 S ATOM 29231 SG CYS H 241 73.634 20.939 105.376 1.00 23.36 S ATOM 29270 SG CYS H 244 71.664 17.731 104.771 1.00 24.37 S ATOM 29590 SG CYS H 266 70.215 21.016 103.782 1.00 20.77 S ATOM 29670 SG CYS H 272 70.760 20.216 107.577 1.00 23.05 S Time building chain proxies: 20.96, per 1000 atoms: 0.47 Number of scatterers: 44690 At special positions: 0 Unit cell: (114.611, 127.028, 157.591, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 96 16.00 P 8 15.00 Mg 2 11.99 O 4260 8.00 N 4006 7.00 C 14074 6.00 H 22240 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.37 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 241 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 244 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 266 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 272 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 333 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5356 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 26 sheets defined 46.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.422A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 135 Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 116 through 120 removed outlier: 4.039A pdb=" N GLY B 120 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.556A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 188 through 199 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.674A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 353 Processing helix chain 'D' and resid 8 through 12 removed outlier: 4.120A pdb=" N LEU D 12 " --> pdb=" O PHE D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.020A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 189 through 197 Proline residue: D 194 - end of helix Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.422A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 135 Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 81 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 4.039A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 85 removed outlier: 3.556A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU G 85 " --> pdb=" O TYR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 199 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 281 through 295 Processing helix chain 'G' and resid 296 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.674A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 333 through 353 Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.120A pdb=" N LEU H 12 " --> pdb=" O PHE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 137 through 147 removed outlier: 4.019A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 Processing helix chain 'H' and resid 189 through 197 Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 268 through 279 Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 101 through 113 removed outlier: 4.392A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 removed outlier: 3.628A pdb=" N ILE I 139 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 196 Processing helix chain 'I' and resid 205 through 213 Processing helix chain 'I' and resid 230 through 236 Processing helix chain 'I' and resid 239 through 248 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 73 through 84 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.393A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 135 through 139 removed outlier: 3.628A pdb=" N ILE J 139 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 Processing helix chain 'J' and resid 147 through 161 Processing helix chain 'J' and resid 177 through 196 Processing helix chain 'J' and resid 205 through 213 Processing helix chain 'J' and resid 230 through 236 Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 80 through 91 Processing helix chain 'K' and resid 106 through 117 Proline residue: K 114 - end of helix Processing helix chain 'K' and resid 121 through 136 Processing helix chain 'K' and resid 139 through 143 Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 151 through 164 Processing helix chain 'K' and resid 181 through 199 Processing helix chain 'K' and resid 208 through 216 Processing helix chain 'L' and resid 46 through 55 Processing helix chain 'L' and resid 80 through 91 Processing helix chain 'L' and resid 106 through 117 Proline residue: L 114 - end of helix Processing helix chain 'L' and resid 121 through 136 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 151 through 164 Processing helix chain 'L' and resid 181 through 199 Processing helix chain 'L' and resid 208 through 216 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 5.338A pdb=" N PHE A 61 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 51 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 63 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA A 71 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA A 41 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ARG A 73 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 39 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 88 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 46 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL C 90 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLN A 48 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 removed outlier: 4.441A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.776A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.631A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS C 268 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.370A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AB1, first strand: chain 'D' and resid 251 through 255 Processing sheet with id=AB2, first strand: chain 'E' and resid 79 through 85 removed outlier: 5.338A pdb=" N PHE E 61 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA E 51 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY E 63 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA E 71 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA E 41 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG E 73 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 39 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU G 88 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU E 46 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL G 90 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN E 48 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.452A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.775A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.632A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.370A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR H 106 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB9, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 28 removed outlier: 3.611A pdb=" N ALA I 16 " --> pdb=" O LYS I 19 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE I 21 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU I 14 " --> pdb=" O PHE I 21 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP I 23 " --> pdb=" O THR I 12 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR I 12 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER I 25 " --> pdb=" O ASN I 10 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN I 10 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASP I 27 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL I 8 " --> pdb=" O ASP I 27 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU I 11 " --> pdb=" O GLN I 59 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN I 59 " --> pdb=" O LEU I 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 85 through 88 removed outlier: 6.401A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL I 167 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL I 202 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET I 169 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL I 218 " --> pdb=" O VAL I 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 19 through 28 removed outlier: 3.611A pdb=" N ALA J 16 " --> pdb=" O LYS J 19 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE J 21 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU J 14 " --> pdb=" O PHE J 21 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP J 23 " --> pdb=" O THR J 12 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR J 12 " --> pdb=" O ASP J 23 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER J 25 " --> pdb=" O ASN J 10 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN J 10 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP J 27 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL J 8 " --> pdb=" O ASP J 27 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU J 11 " --> pdb=" O GLN J 59 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN J 59 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 85 through 88 removed outlier: 6.402A pdb=" N GLY J 86 " --> pdb=" O PHE J 168 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP J 170 " --> pdb=" O GLY J 86 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL J 88 " --> pdb=" O ASP J 170 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL J 167 " --> pdb=" O VAL J 200 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL J 202 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET J 169 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU J 216 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER J 227 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL J 218 " --> pdb=" O VAL J 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 20 through 31 removed outlier: 6.071A pdb=" N LYS K 9 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN K 25 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL K 7 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA K 27 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN K 5 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU K 29 " --> pdb=" O ASN K 3 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN K 3 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL K 7 " --> pdb=" O GLU K 62 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU K 62 " --> pdb=" O VAL K 7 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 92 through 95 removed outlier: 6.568A pdb=" N GLY K 93 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP K 174 " --> pdb=" O GLY K 93 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL K 95 " --> pdb=" O ASP K 174 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 20 through 31 removed outlier: 6.072A pdb=" N LYS L 9 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN L 25 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL L 7 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA L 27 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN L 5 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU L 29 " --> pdb=" O ASN L 3 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN L 3 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL L 7 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU L 62 " --> pdb=" O VAL L 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 92 through 95 removed outlier: 6.568A pdb=" N GLY L 93 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP L 174 " --> pdb=" O GLY L 93 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL L 95 " --> pdb=" O ASP L 174 " (cutoff:3.500A) 1091 hydrogen bonds defined for protein. 3015 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: 18.07 Time building geometry restraints manager: 14.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22224 1.02 - 1.22: 20 1.22 - 1.42: 9295 1.42 - 1.62: 13391 1.62 - 1.81: 182 Bond restraints: 45112 Sorted by residual: bond pdb=" C2' ANP I1002 " pdb=" C3' ANP I1002 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C2' ANP J1002 " pdb=" C3' ANP J1002 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3' ANP I1002 " pdb=" O3' ANP I1002 " ideal model delta sigma weight residual 1.386 1.566 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C3' ANP J1002 " pdb=" O3' ANP J1002 " ideal model delta sigma weight residual 1.386 1.566 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C1' ANP I1002 " pdb=" C2' ANP I1002 " ideal model delta sigma weight residual 1.542 1.679 -0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 45107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.30: 81481 7.30 - 14.61: 27 14.61 - 21.91: 6 21.91 - 29.21: 13 29.21 - 36.52: 21 Bond angle restraints: 81548 Sorted by residual: angle pdb=" N THR F 2 " pdb=" CA THR F 2 " pdb=" HA THR F 2 " ideal model delta sigma weight residual 110.00 73.48 36.52 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 110.00 73.52 36.48 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 110.00 73.57 36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CB ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 109.00 72.84 36.16 3.00e+00 1.11e-01 1.45e+02 ... (remaining 81543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19400 17.84 - 35.68: 1140 35.68 - 53.52: 473 53.52 - 71.36: 145 71.36 - 89.20: 66 Dihedral angle restraints: 21224 sinusoidal: 11818 harmonic: 9406 Sorted by residual: dihedral pdb=" CA ARG G 100 " pdb=" C ARG G 100 " pdb=" N LEU G 101 " pdb=" CA LEU G 101 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG C 100 " pdb=" C ARG C 100 " pdb=" N LEU C 101 " pdb=" CA LEU C 101 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA LEU B 130 " pdb=" C LEU B 130 " pdb=" N SER B 131 " pdb=" CA SER B 131 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 21221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3393 0.104 - 0.208: 148 0.208 - 0.312: 11 0.312 - 0.416: 0 0.416 - 0.521: 4 Chirality restraints: 3556 Sorted by residual: chirality pdb=" CB THR F 5 " pdb=" CA THR F 5 " pdb=" OG1 THR F 5 " pdb=" CG2 THR F 5 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CB THR B 5 " pdb=" CA THR B 5 " pdb=" OG1 THR B 5 " pdb=" CG2 THR B 5 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB THR F 2 " pdb=" CA THR F 2 " pdb=" OG1 THR F 2 " pdb=" CG2 THR F 2 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3553 not shown) Planarity restraints: 6800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 98 " -0.043 2.00e-02 2.50e+03 4.07e-02 4.96e+01 pdb=" CG PHE L 98 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE L 98 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE L 98 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE L 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE L 98 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE L 98 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE L 98 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE L 98 " 0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE L 98 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE L 98 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE L 98 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 98 " 0.030 2.00e-02 2.50e+03 3.63e-02 3.95e+01 pdb=" CG PHE K 98 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 PHE K 98 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 98 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE K 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 98 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 98 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE K 98 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE K 98 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE K 98 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE K 98 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE K 98 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 156 " -0.016 2.00e-02 2.50e+03 4.56e-02 3.12e+01 pdb=" CD GLN K 156 " 0.080 2.00e-02 2.50e+03 pdb=" OE1 GLN K 156 " -0.047 2.00e-02 2.50e+03 pdb=" NE2 GLN K 156 " 0.039 2.00e-02 2.50e+03 pdb="HE21 GLN K 156 " -0.045 2.00e-02 2.50e+03 pdb="HE22 GLN K 156 " -0.010 2.00e-02 2.50e+03 ... (remaining 6797 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1014 2.09 - 2.72: 76812 2.72 - 3.34: 139666 3.34 - 3.97: 183420 3.97 - 4.60: 284085 Nonbonded interactions: 684997 Sorted by model distance: nonbonded pdb=" OE2 GLU A 58 " pdb=" H SER C 171 " model vdw 1.460 2.450 nonbonded pdb=" OE2 GLU E 58 " pdb=" H SER G 171 " model vdw 1.463 2.450 nonbonded pdb=" OE2 GLU A 37 " pdb="HH11 ARG A 73 " model vdw 1.509 2.450 nonbonded pdb=" OE2 GLU E 37 " pdb="HH11 ARG E 73 " model vdw 1.518 2.450 nonbonded pdb=" OD1 ASP G 95 " pdb=" HG1 THR G 97 " model vdw 1.570 2.450 ... (remaining 684992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 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: 5.830 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: 0.770 Extract box with map and model: 1.620 Check model and map are aligned: 0.310 Set scattering table: 0.420 Process input model: 110.410 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.006 0.295 22872 Z= 0.336 Angle : 0.726 27.099 31096 Z= 0.353 Chirality : 0.048 0.521 3556 Planarity : 0.005 0.090 4086 Dihedral : 14.766 89.199 8542 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.04 % Allowed : 6.89 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.45 (0.16), residues: 2858 helix: 1.82 (0.16), residues: 1134 sheet: 0.26 (0.23), residues: 490 loop : 0.61 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 11 HIS 0.015 0.001 HIS L 144 PHE 0.094 0.002 PHE K 98 TYR 0.034 0.002 TYR L 58 ARG 0.022 0.001 ARG L 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 444 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 419 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8659 (ttt) cc_final: 0.8280 (ttt) REVERT: H 153 MET cc_start: 0.8396 (tpp) cc_final: 0.8190 (tpp) REVERT: K 74 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8387 (t) REVERT: L 74 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8356 (t) REVERT: L 144 HIS cc_start: 0.7724 (m-70) cc_final: 0.7522 (m-70) outliers start: 25 outliers final: 8 residues processed: 433 average time/residue: 3.0290 time to fit residues: 1510.1730 Evaluate side-chains 327 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 317 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 257 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN B 107 ASN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN E 19 GLN E 28 ASN E 90 GLN F 107 ASN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN I 3 GLN I 89 HIS J 89 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22872 Z= 0.199 Angle : 0.550 11.192 31096 Z= 0.287 Chirality : 0.053 1.339 3556 Planarity : 0.005 0.057 4086 Dihedral : 7.465 67.104 3222 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.17 % Allowed : 9.40 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.48 (0.16), residues: 2858 helix: 1.87 (0.16), residues: 1148 sheet: 0.11 (0.23), residues: 492 loop : 0.66 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 11 HIS 0.006 0.001 HIS L 144 PHE 0.011 0.001 PHE F 18 TYR 0.022 0.001 TYR I 241 ARG 0.006 0.001 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 153 MET cc_start: 0.8597 (tpp) cc_final: 0.8303 (tpp) REVERT: K 74 VAL cc_start: 0.8641 (t) cc_final: 0.8404 (t) REVERT: K 89 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7880 (tttm) REVERT: K 219 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (tp) REVERT: L 10 THR cc_start: 0.7098 (p) cc_final: 0.6617 (t) REVERT: L 74 VAL cc_start: 0.8586 (t) cc_final: 0.8286 (t) outliers start: 28 outliers final: 12 residues processed: 338 average time/residue: 3.1788 time to fit residues: 1235.4423 Evaluate side-chains 322 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 309 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 159 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN B 74 ASN C 149 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 90 GLN F 74 ASN G 149 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 159 ASN L 156 GLN L 159 ASN L 207 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22872 Z= 0.241 Angle : 0.542 10.943 31096 Z= 0.283 Chirality : 0.054 1.325 3556 Planarity : 0.004 0.046 4086 Dihedral : 7.396 63.924 3216 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.96 % Allowed : 10.19 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.47 (0.16), residues: 2858 helix: 1.91 (0.16), residues: 1144 sheet: 0.05 (0.23), residues: 488 loop : 0.63 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 11 HIS 0.005 0.001 HIS G 316 PHE 0.014 0.001 PHE B 18 TYR 0.019 0.002 TYR I 241 ARG 0.004 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 316 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8744 (ttt) cc_final: 0.8300 (ttt) REVERT: G 287 MET cc_start: 0.8742 (ttt) cc_final: 0.8309 (ttt) REVERT: H 153 MET cc_start: 0.8603 (tpp) cc_final: 0.8233 (tpp) REVERT: I 111 MET cc_start: 0.8731 (mtm) cc_final: 0.8482 (mtm) REVERT: J 111 MET cc_start: 0.8766 (mtm) cc_final: 0.8511 (mtm) REVERT: K 74 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8395 (t) REVERT: K 89 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7961 (tppt) REVERT: L 10 THR cc_start: 0.7188 (p) cc_final: 0.6683 (t) REVERT: L 74 VAL cc_start: 0.8665 (t) cc_final: 0.8392 (t) outliers start: 23 outliers final: 7 residues processed: 327 average time/residue: 3.3002 time to fit residues: 1231.7578 Evaluate side-chains 308 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 300 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN A 131 GLN C 149 GLN E 19 GLN E 28 ASN E 90 GLN E 131 GLN G 149 GLN I 3 GLN I 66 ASN I 223 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22872 Z= 0.242 Angle : 0.539 11.084 31096 Z= 0.281 Chirality : 0.054 1.378 3556 Planarity : 0.004 0.045 4086 Dihedral : 7.148 61.478 3216 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.84 % Allowed : 10.07 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.46 (0.16), residues: 2858 helix: 1.93 (0.16), residues: 1144 sheet: 0.01 (0.24), residues: 496 loop : 0.62 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 11 HIS 0.005 0.001 HIS C 316 PHE 0.014 0.001 PHE B 18 TYR 0.018 0.002 TYR J 241 ARG 0.003 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 320 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 300 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.8521 (tpp) cc_final: 0.8164 (tpp) REVERT: H 153 MET cc_start: 0.8610 (tpp) cc_final: 0.8246 (tpp) REVERT: I 32 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: I 189 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8101 (mmp-170) REVERT: J 32 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: J 111 MET cc_start: 0.8773 (mtm) cc_final: 0.8493 (mtm) REVERT: J 189 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8105 (mmp-170) REVERT: J 251 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6710 (mm110) REVERT: K 74 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8400 (t) REVERT: K 89 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7968 (tppt) REVERT: K 109 GLU cc_start: 0.8021 (mp0) cc_final: 0.7801 (mp0) REVERT: L 10 THR cc_start: 0.7267 (p) cc_final: 0.6772 (t) REVERT: L 74 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8394 (t) REVERT: L 109 GLU cc_start: 0.8026 (mp0) cc_final: 0.7819 (mp0) outliers start: 20 outliers final: 6 residues processed: 309 average time/residue: 3.2340 time to fit residues: 1144.6610 Evaluate side-chains 306 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 294 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN E 19 GLN E 90 GLN G 149 GLN J 223 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 22872 Z= 0.379 Angle : 0.587 10.987 31096 Z= 0.310 Chirality : 0.056 1.376 3556 Planarity : 0.005 0.059 4086 Dihedral : 7.410 61.394 3214 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.96 % Allowed : 10.69 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.26 (0.16), residues: 2858 helix: 1.71 (0.15), residues: 1144 sheet: -0.03 (0.24), residues: 484 loop : 0.53 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 11 HIS 0.005 0.001 HIS J 13 PHE 0.017 0.002 PHE B 18 TYR 0.018 0.002 TYR J 241 ARG 0.009 0.001 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 4.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8701 (ttt) cc_final: 0.8351 (ttt) REVERT: D 153 MET cc_start: 0.8565 (tpp) cc_final: 0.8176 (tpp) REVERT: G 287 MET cc_start: 0.8699 (ttt) cc_final: 0.8358 (ttt) REVERT: I 111 MET cc_start: 0.8807 (mtm) cc_final: 0.8393 (mtm) REVERT: I 189 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8170 (mmp-170) REVERT: J 32 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: J 111 MET cc_start: 0.8865 (mtm) cc_final: 0.8509 (mtm) REVERT: J 189 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8169 (mmp-170) REVERT: K 74 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8414 (t) REVERT: K 89 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8079 (tppt) REVERT: K 109 GLU cc_start: 0.8198 (mp0) cc_final: 0.7769 (mp0) REVERT: L 10 THR cc_start: 0.7351 (p) cc_final: 0.6835 (t) REVERT: L 74 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8394 (t) REVERT: L 109 GLU cc_start: 0.8197 (mp0) cc_final: 0.7790 (mp0) outliers start: 23 outliers final: 7 residues processed: 298 average time/residue: 3.2160 time to fit residues: 1096.9315 Evaluate side-chains 293 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 281 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 274 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN C 150 GLN E 19 GLN E 28 ASN E 90 GLN G 149 GLN G 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22872 Z= 0.185 Angle : 0.529 11.277 31096 Z= 0.275 Chirality : 0.054 1.400 3556 Planarity : 0.004 0.045 4086 Dihedral : 6.629 58.586 3214 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.88 % Allowed : 10.90 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2858 helix: 1.93 (0.16), residues: 1144 sheet: -0.11 (0.24), residues: 494 loop : 0.56 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 11 HIS 0.003 0.001 HIS G 316 PHE 0.012 0.001 PHE B 18 TYR 0.017 0.002 TYR D 214 ARG 0.004 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.8570 (tpp) cc_final: 0.8202 (tpp) REVERT: D 196 MET cc_start: 0.8586 (mtp) cc_final: 0.8328 (mtp) REVERT: I 189 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7944 (mmp-170) REVERT: J 32 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: J 111 MET cc_start: 0.8778 (mtm) cc_final: 0.8564 (mtm) REVERT: J 189 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7940 (mmp-170) REVERT: J 251 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6734 (mm-40) REVERT: K 74 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8445 (t) REVERT: K 89 LYS cc_start: 0.8255 (ttmt) cc_final: 0.8026 (tppt) REVERT: K 109 GLU cc_start: 0.8217 (mp0) cc_final: 0.7778 (mp0) REVERT: L 10 THR cc_start: 0.7427 (p) cc_final: 0.6890 (t) REVERT: L 74 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8404 (t) REVERT: L 109 GLU cc_start: 0.8266 (mp0) cc_final: 0.7828 (mp0) outliers start: 21 outliers final: 10 residues processed: 289 average time/residue: 3.2108 time to fit residues: 1066.7085 Evaluate side-chains 289 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 273 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 149 GLN C 150 GLN E 90 GLN G 149 GLN G 150 GLN I 66 ASN ** K 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22872 Z= 0.243 Angle : 0.535 11.141 31096 Z= 0.279 Chirality : 0.054 1.386 3556 Planarity : 0.004 0.044 4086 Dihedral : 6.041 60.089 3214 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.00 % Allowed : 10.94 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.39 (0.16), residues: 2858 helix: 1.92 (0.16), residues: 1144 sheet: -0.13 (0.24), residues: 494 loop : 0.57 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 11 HIS 0.004 0.001 HIS G 316 PHE 0.014 0.001 PHE B 18 TYR 0.018 0.002 TYR I 241 ARG 0.005 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.8594 (tpp) cc_final: 0.8208 (tpp) REVERT: I 189 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7952 (mmp-170) REVERT: J 32 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: J 111 MET cc_start: 0.8824 (mtm) cc_final: 0.8608 (mtm) REVERT: J 189 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7955 (mmp-170) REVERT: J 251 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6778 (mm-40) REVERT: K 74 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8475 (t) REVERT: K 109 GLU cc_start: 0.8258 (mp0) cc_final: 0.7759 (mp0) REVERT: L 10 THR cc_start: 0.7415 (p) cc_final: 0.6893 (t) REVERT: L 74 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8432 (t) REVERT: L 109 GLU cc_start: 0.8262 (mp0) cc_final: 0.7773 (mp0) outliers start: 24 outliers final: 11 residues processed: 294 average time/residue: 3.1446 time to fit residues: 1061.9267 Evaluate side-chains 289 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 273 time to evaluate : 3.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 156 GLN Chi-restraints excluded: chain L residue 159 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 0.0970 chunk 186 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 215 optimal weight: 0.1980 chunk 249 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN C 150 GLN E 19 GLN E 90 GLN G 149 GLN G 150 GLN I 66 ASN K 159 ASN L 159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22872 Z= 0.157 Angle : 0.515 11.299 31096 Z= 0.267 Chirality : 0.054 1.401 3556 Planarity : 0.004 0.044 4086 Dihedral : 5.643 59.525 3214 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.63 % Allowed : 11.49 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.48 (0.16), residues: 2858 helix: 2.03 (0.16), residues: 1148 sheet: -0.16 (0.24), residues: 494 loop : 0.61 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 11 HIS 0.003 0.001 HIS C 316 PHE 0.010 0.001 PHE B 18 TYR 0.016 0.001 TYR I 241 ARG 0.005 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 282 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.8593 (tpp) cc_final: 0.8217 (tpp) REVERT: D 196 MET cc_start: 0.8584 (mtp) cc_final: 0.8370 (mtp) REVERT: E 124 MET cc_start: 0.7751 (mmp) cc_final: 0.7515 (mmt) REVERT: I 189 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7781 (mmp-170) REVERT: J 189 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8103 (mmp-170) REVERT: K 74 VAL cc_start: 0.8693 (t) cc_final: 0.8483 (t) REVERT: K 109 GLU cc_start: 0.8275 (mp0) cc_final: 0.7755 (mp0) REVERT: L 10 THR cc_start: 0.7420 (p) cc_final: 0.6899 (t) REVERT: L 74 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8442 (t) REVERT: L 109 GLU cc_start: 0.8273 (mp0) cc_final: 0.7758 (mp0) outliers start: 15 outliers final: 9 residues processed: 291 average time/residue: 3.2010 time to fit residues: 1069.4896 Evaluate side-chains 282 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 156 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 200 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 254 optimal weight: 0.4980 chunk 167 optimal weight: 0.0970 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 149 GLN C 150 GLN E 90 GLN G 149 GLN G 150 GLN I 66 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22872 Z= 0.254 Angle : 0.544 11.106 31096 Z= 0.282 Chirality : 0.054 1.383 3556 Planarity : 0.004 0.044 4086 Dihedral : 5.599 59.990 3214 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.58 % Allowed : 11.74 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.43 (0.16), residues: 2858 helix: 1.98 (0.16), residues: 1144 sheet: -0.17 (0.24), residues: 496 loop : 0.61 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 11 HIS 0.004 0.001 HIS I 13 PHE 0.014 0.002 PHE F 18 TYR 0.015 0.002 TYR I 241 ARG 0.004 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 277 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.8597 (tpp) cc_final: 0.8210 (tpp) REVERT: I 189 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7885 (mmp-170) REVERT: J 189 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7887 (mmp-170) REVERT: J 251 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6824 (mm-40) REVERT: K 74 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8470 (t) REVERT: K 109 GLU cc_start: 0.8275 (mp0) cc_final: 0.7738 (mp0) REVERT: K 167 ASP cc_start: 0.8136 (m-30) cc_final: 0.7887 (m-30) REVERT: L 10 THR cc_start: 0.7428 (p) cc_final: 0.6904 (t) REVERT: L 74 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8459 (t) REVERT: L 109 GLU cc_start: 0.8281 (mp0) cc_final: 0.7751 (mp0) outliers start: 14 outliers final: 6 residues processed: 284 average time/residue: 3.1418 time to fit residues: 1023.9801 Evaluate side-chains 279 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 269 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 156 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN C 150 GLN E 19 GLN E 90 GLN G 149 GLN G 150 GLN K 57 ASN L 57 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22872 Z= 0.183 Angle : 0.524 11.286 31096 Z= 0.271 Chirality : 0.054 1.406 3556 Planarity : 0.004 0.044 4086 Dihedral : 5.469 59.425 3214 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.46 % Allowed : 11.86 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.47 (0.16), residues: 2858 helix: 2.02 (0.16), residues: 1148 sheet: -0.16 (0.24), residues: 494 loop : 0.61 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 11 HIS 0.003 0.001 HIS C 316 PHE 0.011 0.001 PHE F 18 TYR 0.016 0.001 TYR J 241 ARG 0.004 0.000 ARG I 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 280 time to evaluate : 3.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 153 MET cc_start: 0.8594 (tpp) cc_final: 0.8211 (tpp) REVERT: E 124 MET cc_start: 0.7764 (mmp) cc_final: 0.7523 (mmt) REVERT: I 189 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7783 (mmp-170) REVERT: J 189 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7786 (mmp-170) REVERT: J 251 GLN cc_start: 0.7014 (mm-40) cc_final: 0.6806 (mm-40) REVERT: K 74 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8483 (t) REVERT: K 109 GLU cc_start: 0.8283 (mp0) cc_final: 0.7735 (mp0) REVERT: K 167 ASP cc_start: 0.8133 (m-30) cc_final: 0.7900 (m-30) REVERT: L 10 THR cc_start: 0.7428 (p) cc_final: 0.6905 (t) REVERT: L 74 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (t) REVERT: L 109 GLU cc_start: 0.8293 (mp0) cc_final: 0.7752 (mp0) outliers start: 11 outliers final: 5 residues processed: 285 average time/residue: 3.1625 time to fit residues: 1039.6552 Evaluate side-chains 279 residues out of total 2396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 149 GLN C 150 GLN E 90 GLN G 149 GLN G 150 GLN I 66 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.106868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.077635 restraints weight = 81631.152| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.58 r_work: 0.2900 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22872 Z= 0.345 Angle : 0.577 11.069 31096 Z= 0.303 Chirality : 0.055 1.381 3556 Planarity : 0.005 0.045 4086 Dihedral : 5.614 60.415 3214 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.46 % Allowed : 11.82 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.27 (0.16), residues: 2858 helix: 1.82 (0.15), residues: 1144 sheet: -0.22 (0.24), residues: 484 loop : 0.51 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 11 HIS 0.005 0.001 HIS J 13 PHE 0.017 0.002 PHE F 18 TYR 0.015 0.002 TYR J 241 ARG 0.005 0.001 ARG J 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17290.09 seconds wall clock time: 309 minutes 1.76 seconds (18541.76 seconds total)