Starting phenix.real_space_refine on Fri Mar 22 03:31:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/03_2024/8c5z_16445.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/03_2024/8c5z_16445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/03_2024/8c5z_16445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/03_2024/8c5z_16445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/03_2024/8c5z_16445.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/03_2024/8c5z_16445.pdb" } resolution = 3.8 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= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15650 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 49 5.16 5 C 10603 2.51 5 N 2825 2.21 5 O 3134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 13": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16615 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2837 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 14, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "G" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "H" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "I" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 919 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "J" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1408 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain: "K" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1474 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain: "L" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 897 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "A" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1715 SG CYS A 218 79.987 32.891 94.445 1.00 93.17 S ATOM 1737 SG CYS A 221 77.516 30.716 96.246 1.00 89.99 S ATOM 1859 SG CYS A 236 80.913 31.491 97.883 1.00 89.99 S ATOM 5516 SG CYS D 218 24.729 50.501 14.031 1.00247.06 S ATOM 5538 SG CYS D 221 27.606 51.827 12.165 1.00253.91 S ATOM 5660 SG CYS D 236 24.206 53.714 12.090 1.00271.18 S ATOM 9317 SG CYS G 218 83.762 106.958 59.518 1.00250.81 S ATOM 9339 SG CYS G 221 81.281 109.065 57.608 1.00243.72 S ATOM 9461 SG CYS G 236 84.384 107.630 55.798 1.00262.56 S ATOM 13118 SG CYS J 218 21.839 83.167 146.406 1.00200.54 S ATOM 13140 SG CYS J 221 24.129 80.503 147.875 1.00223.35 S ATOM 13262 SG CYS J 236 20.385 79.733 147.138 1.00224.74 S Time building chain proxies: 8.79, per 1000 atoms: 0.53 Number of scatterers: 16615 At special positions: 0 Unit cell: (104.92, 124.7, 161.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 49 16.00 O 3134 8.00 N 2825 7.00 C 10603 6.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 239 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 218 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 221 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 236 " pdb=" ZN D 500 " pdb="ZN ZN D 500 " - pdb=" ND1 HIS D 239 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 221 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 218 " pdb="ZN ZN D 500 " - pdb=" SG CYS D 236 " pdb=" ZN G 500 " pdb="ZN ZN G 500 " - pdb=" ND1 HIS G 239 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 218 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 221 " pdb="ZN ZN G 500 " - pdb=" SG CYS G 236 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 239 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 218 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 236 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 221 " Number of angles added : 12 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3788 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 21 sheets defined 34.1% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.638A pdb=" N MET A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 54 through 58 removed outlier: 4.611A pdb=" N GLU A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 122 through 128 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.599A pdb=" N GLU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.899A pdb=" N ILE A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.758A pdb=" N GLU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 4.125A pdb=" N ILE A 310 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 311 " --> pdb=" O TYR A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 341 through 356 Processing helix chain 'B' and resid 11 through 16 Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.686A pdb=" N LYS B 83 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 removed outlier: 4.173A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'C' and resid 15 through 19 Processing helix chain 'C' and resid 93 through 112 Proline residue: C 109 - end of helix Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 267 through 275 removed outlier: 3.528A pdb=" N GLU D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 290 removed outlier: 3.588A pdb=" N ILE D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 307 Processing helix chain 'D' and resid 341 through 356 Processing helix chain 'E' and resid 11 through 17 Processing helix chain 'E' and resid 81 through 86 removed outlier: 3.943A pdb=" N ALA E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 150 removed outlier: 3.645A pdb=" N TRP E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR E 150 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 167 through 181 removed outlier: 4.137A pdb=" N GLU E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 94 through 112 Proline residue: F 109 - end of helix removed outlier: 4.161A pdb=" N GLU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 267 through 275 Processing helix chain 'G' and resid 277 through 290 Processing helix chain 'G' and resid 294 through 306 removed outlier: 3.568A pdb=" N GLU G 306 " --> pdb=" O LEU G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 311 removed outlier: 4.106A pdb=" N ILE G 310 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE G 311 " --> pdb=" O TYR G 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 307 through 311' Processing helix chain 'G' and resid 340 through 356 removed outlier: 3.502A pdb=" N GLU G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 17 Processing helix chain 'H' and resid 80 through 87 removed outlier: 3.958A pdb=" N LYS H 83 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 151 removed outlier: 4.349A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE H 146 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR H 150 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 163 Processing helix chain 'H' and resid 166 through 181 removed outlier: 4.269A pdb=" N LEU H 170 " --> pdb=" O GLU H 166 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 19 Processing helix chain 'I' and resid 93 through 112 removed outlier: 3.760A pdb=" N LEU I 97 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Proline residue: I 109 - end of helix Processing helix chain 'J' and resid 189 through 193 Processing helix chain 'J' and resid 267 through 275 Processing helix chain 'J' and resid 277 through 290 removed outlier: 3.691A pdb=" N ILE J 281 " --> pdb=" O SER J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 307 Processing helix chain 'J' and resid 340 through 356 removed outlier: 3.508A pdb=" N GLU J 344 " --> pdb=" O ASP J 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 17 Processing helix chain 'K' and resid 81 through 86 removed outlier: 4.106A pdb=" N ALA K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 150 removed outlier: 3.536A pdb=" N TRP K 122 " --> pdb=" O HIS K 118 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU K 145 " --> pdb=" O LYS K 141 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE K 146 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR K 150 " --> pdb=" O ILE K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 167 through 181 removed outlier: 3.800A pdb=" N GLU K 171 " --> pdb=" O GLU K 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 19 removed outlier: 3.663A pdb=" N ILE L 19 " --> pdb=" O ILE L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 114 Proline residue: L 109 - end of helix removed outlier: 3.745A pdb=" N GLU L 112 " --> pdb=" O LEU L 108 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY L 113 " --> pdb=" O PRO L 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU L 114 " --> pdb=" O ARG L 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 87 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 79 through 87 current: chain 'A' and resid 100 through 109 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 114 through 120 current: chain 'A' and resid 152 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 217 removed outlier: 6.481A pdb=" N ALA A 207 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ASP A 255 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A 209 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY A 253 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N TYR A 260 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU A 331 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG A 262 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA A 333 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 264 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 335 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N PHE A 266 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N GLU A 337 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG A 318 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TRP A 336 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 316 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 227 removed outlier: 3.695A pdb=" N ASP A 226 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 9 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 42 through 49 current: chain 'B' and resid 61 through 67 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 72 through 78 current: chain 'B' and resid 107 through 116 Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 removed outlier: 7.057A pdb=" N VAL C 12 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N ILE C 29 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL C 65 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP C 88 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 67 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE C 86 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE C 69 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE C 79 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE C 52 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 34 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP C 45 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 32 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 186 through 187 removed outlier: 6.344A pdb=" N THR D 186 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ARG D 203 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N GLU D 314 " --> pdb=" O ASP D 338 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASP D 338 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL D 316 " --> pdb=" O TRP D 336 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP D 336 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG D 318 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N TYR D 260 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N LEU D 331 " --> pdb=" O TYR D 260 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG D 262 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA D 333 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR D 264 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N SER D 335 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N PHE D 266 " --> pdb=" O SER D 335 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N GLU D 337 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY D 253 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 209 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASP D 255 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA D 207 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA9, first strand: chain 'E' and resid 8 through 9 removed outlier: 6.628A pdb=" N GLN E 95 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL E 114 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE E 97 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL E 72 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE E 109 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TRP E 74 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL E 111 " --> pdb=" O TRP E 74 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU E 76 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY E 113 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N PHE E 78 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 15.781A pdb=" N SER E 115 " --> pdb=" O PHE E 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 13 removed outlier: 6.537A pdb=" N VAL F 12 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ILE F 29 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL F 65 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP F 88 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG F 67 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE F 86 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE F 69 " --> pdb=" O GLU F 84 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS F 80 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ILE F 79 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE F 52 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET F 41 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL F 35 " --> pdb=" O MET F 41 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TRP F 43 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 186 through 187 removed outlier: 6.073A pdb=" N THR G 186 " --> pdb=" O GLU G 201 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ARG G 203 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL G 316 " --> pdb=" O TRP G 336 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRP G 336 " --> pdb=" O VAL G 316 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG G 318 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N TYR G 260 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N LEU G 331 " --> pdb=" O TYR G 260 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG G 262 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA G 333 " --> pdb=" O ARG G 262 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR G 264 " --> pdb=" O ALA G 333 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER G 335 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N PHE G 266 " --> pdb=" O SER G 335 " (cutoff:3.500A) removed outlier: 11.940A pdb=" N GLU G 337 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY G 253 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL G 209 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP G 255 " --> pdb=" O ALA G 207 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA G 207 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 226 through 228 removed outlier: 3.510A pdb=" N VAL G 233 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 7 through 9 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 42 through 49 current: chain 'H' and resid 61 through 67 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 72 through 78 current: chain 'H' and resid 106 through 116 Processing sheet with id=AB6, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB7, first strand: chain 'I' and resid 12 through 13 removed outlier: 3.567A pdb=" N VAL I 12 " --> pdb=" O ARG I 25 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 27 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL I 65 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ASP I 88 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG I 67 " --> pdb=" O ILE I 86 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE I 86 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE I 69 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS I 80 " --> pdb=" O ILE I 73 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N VAL I 50 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE I 81 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE I 52 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA I 83 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS I 34 " --> pdb=" O TRP I 43 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP I 45 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL I 32 " --> pdb=" O ASP I 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.035A pdb=" N THR J 186 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG J 203 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL J 316 " --> pdb=" O TRP J 336 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP J 336 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ARG J 318 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N TYR J 260 " --> pdb=" O LEU J 329 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU J 331 " --> pdb=" O TYR J 260 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG J 262 " --> pdb=" O LEU J 331 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA J 333 " --> pdb=" O ARG J 262 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR J 264 " --> pdb=" O ALA J 333 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER J 335 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N PHE J 266 " --> pdb=" O SER J 335 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N GLU J 337 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE J 245 " --> pdb=" O ASP J 216 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP J 216 " --> pdb=" O ILE J 245 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET J 247 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N THR J 214 " --> pdb=" O MET J 247 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE J 249 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL J 212 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASP J 251 " --> pdb=" O TYR J 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS J 208 " --> pdb=" O GLY J 253 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP J 255 " --> pdb=" O ILE J 206 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE J 206 " --> pdb=" O ASP J 255 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 226 through 228 removed outlier: 3.603A pdb=" N VAL J 233 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 8 through 9 removed outlier: 6.365A pdb=" N THR K 8 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N VAL K 46 " --> pdb=" O THR K 8 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 43 through 49 current: chain 'K' and resid 61 through 67 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 72 through 78 current: chain 'K' and resid 106 through 116 Processing sheet with id=AC2, first strand: chain 'K' and resid 19 through 21 Processing sheet with id=AC3, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.839A pdb=" N VAL L 12 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE L 29 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL L 65 " --> pdb=" O ASP L 88 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASP L 88 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG L 67 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE L 86 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE L 69 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS L 80 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN L 75 " --> pdb=" O GLY L 78 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY L 78 " --> pdb=" O ASN L 75 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ILE L 79 " --> pdb=" O VAL L 50 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ILE L 52 " --> pdb=" O ILE L 79 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA L 83 " --> pdb=" O GLU L 54 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET L 41 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL L 35 " --> pdb=" O MET L 41 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N TRP L 43 " --> pdb=" O ILE L 33 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 6.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5510 1.34 - 1.46: 3400 1.46 - 1.58: 7867 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 16863 Sorted by residual: bond pdb=" N ALA L 92 " pdb=" CA ALA L 92 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.27e-02 6.20e+03 1.13e+01 bond pdb=" CA ALA L 92 " pdb=" C ALA L 92 " ideal model delta sigma weight residual 1.528 1.561 -0.034 1.33e-02 5.65e+03 6.35e+00 bond pdb=" N ASP L 93 " pdb=" CA ASP L 93 " ideal model delta sigma weight residual 1.455 1.481 -0.027 1.36e-02 5.41e+03 3.81e+00 bond pdb=" CG GLU A 283 " pdb=" CD GLU A 283 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CG GLU J 290 " pdb=" CD GLU J 290 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.86e+00 ... (remaining 16858 not shown) Histogram of bond angle deviations from ideal: 96.37 - 104.03: 154 104.03 - 111.68: 7704 111.68 - 119.34: 6674 119.34 - 126.99: 8013 126.99 - 134.64: 138 Bond angle restraints: 22683 Sorted by residual: angle pdb=" N ALA L 92 " pdb=" CA ALA L 92 " pdb=" C ALA L 92 " ideal model delta sigma weight residual 110.35 121.26 -10.91 1.38e+00 5.25e-01 6.25e+01 angle pdb=" C ARG K 79 " pdb=" CA ARG K 79 " pdb=" CB ARG K 79 " ideal model delta sigma weight residual 117.23 108.19 9.04 1.36e+00 5.41e-01 4.42e+01 angle pdb=" CA ARG K 79 " pdb=" C ARG K 79 " pdb=" N ASP K 80 " ideal model delta sigma weight residual 119.98 115.76 4.22 8.50e-01 1.38e+00 2.46e+01 angle pdb=" C GLU J 289 " pdb=" N GLU J 290 " pdb=" CA GLU J 290 " ideal model delta sigma weight residual 121.18 113.30 7.88 1.98e+00 2.55e-01 1.58e+01 angle pdb=" N GLU A 283 " pdb=" CA GLU A 283 " pdb=" CB GLU A 283 " ideal model delta sigma weight residual 110.28 116.30 -6.02 1.55e+00 4.16e-01 1.51e+01 ... (remaining 22678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9270 18.01 - 36.01: 917 36.01 - 54.02: 137 54.02 - 72.03: 16 72.03 - 90.03: 18 Dihedral angle restraints: 10358 sinusoidal: 4456 harmonic: 5902 Sorted by residual: dihedral pdb=" CA LEU C 107 " pdb=" C LEU C 107 " pdb=" N LEU C 108 " pdb=" CA LEU C 108 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PHE J 266 " pdb=" C PHE J 266 " pdb=" N GLY J 267 " pdb=" CA GLY J 267 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU L 107 " pdb=" C LEU L 107 " pdb=" N LEU L 108 " pdb=" CA LEU L 108 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 10355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2170 0.074 - 0.148: 357 0.148 - 0.223: 9 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 2537 Sorted by residual: chirality pdb=" CA TYR A 341 " pdb=" N TYR A 341 " pdb=" C TYR A 341 " pdb=" CB TYR A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA GLU J 289 " pdb=" N GLU J 289 " pdb=" C GLU J 289 " pdb=" CB GLU J 289 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 2534 not shown) Planarity restraints: 2890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 108 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO F 109 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 109 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 109 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 122 " 0.013 2.00e-02 2.50e+03 1.16e-02 3.39e+00 pdb=" CG TRP K 122 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP K 122 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP K 122 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 122 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 122 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 122 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 122 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 122 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP K 122 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 26 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C ASP E 26 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP E 26 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE E 27 " 0.010 2.00e-02 2.50e+03 ... (remaining 2887 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 226 2.63 - 3.20: 14959 3.20 - 3.77: 25147 3.77 - 4.33: 33407 4.33 - 4.90: 54388 Nonbonded interactions: 128127 Sorted by model distance: nonbonded pdb=" CD2 TYR A 341 " pdb=" CB ASN B 120 " model vdw 2.063 3.740 nonbonded pdb=" OE1 GLU J 350 " pdb=" NZ LYS J 354 " model vdw 2.136 2.520 nonbonded pdb=" O THR H 153 " pdb=" OG SER H 156 " model vdw 2.144 2.440 nonbonded pdb=" O LEU G 288 " pdb=" OG SER G 291 " model vdw 2.153 2.440 nonbonded pdb=" OG SER A 277 " pdb=" OE1 GLU A 280 " model vdw 2.157 2.440 ... (remaining 128122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = (chain 'C' and resid 8 through 117) selection = (chain 'F' and resid 8 through 117) selection = (chain 'I' and resid 8 through 117) selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 12.470 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 44.470 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.004 0.043 16863 Z= 0.254 Angle : 0.702 13.235 22683 Z= 0.394 Chirality : 0.050 0.371 2537 Planarity : 0.004 0.056 2890 Dihedral : 14.174 90.034 6570 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.07 % Favored : 96.68 % Rotamer: Outliers : 0.17 % Allowed : 0.22 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2018 helix: 0.96 (0.21), residues: 593 sheet: -0.29 (0.21), residues: 576 loop : -0.50 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP K 122 HIS 0.005 0.001 HIS D 239 PHE 0.021 0.002 PHE J 252 TYR 0.020 0.002 TYR H 127 ARG 0.007 0.000 ARG B 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 383 time to evaluate : 2.049 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8468 (tm-30) REVERT: A 128 TYR cc_start: 0.8420 (t80) cc_final: 0.8163 (t80) REVERT: A 293 LEU cc_start: 0.8585 (mm) cc_final: 0.7893 (mp) REVERT: A 320 ASN cc_start: 0.8291 (t0) cc_final: 0.8087 (t0) REVERT: B 171 GLU cc_start: 0.8895 (pm20) cc_final: 0.8660 (pm20) REVERT: C 41 MET cc_start: 0.6128 (tmm) cc_final: 0.5314 (tmm) REVERT: C 58 ASP cc_start: 0.8036 (t0) cc_final: 0.7134 (m-30) REVERT: C 59 LEU cc_start: 0.6417 (mt) cc_final: 0.4947 (mt) REVERT: C 102 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8896 (tm-30) REVERT: D 265 LEU cc_start: 0.8021 (tp) cc_final: 0.7745 (tp) REVERT: D 295 THR cc_start: 0.8252 (p) cc_final: 0.7730 (t) REVERT: E 181 MET cc_start: 0.6464 (mpp) cc_final: 0.5543 (ttm) REVERT: F 36 ASP cc_start: 0.5628 (p0) cc_final: 0.3774 (p0) REVERT: F 75 ASN cc_start: 0.7603 (m110) cc_final: 0.7277 (p0) REVERT: H 80 ASP cc_start: 0.8615 (t70) cc_final: 0.8385 (t0) REVERT: H 176 LEU cc_start: 0.8951 (tt) cc_final: 0.8459 (tt) REVERT: I 39 ASP cc_start: 0.8485 (m-30) cc_final: 0.8243 (m-30) REVERT: I 106 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9086 (tmtt) REVERT: J 358 MET cc_start: 0.1608 (mpp) cc_final: 0.1070 (mpp) REVERT: K 8 THR cc_start: 0.8939 (m) cc_final: 0.8699 (p) REVERT: K 67 ASP cc_start: 0.7910 (t70) cc_final: 0.7480 (p0) REVERT: K 112 GLU cc_start: 0.7713 (tp30) cc_final: 0.7361 (mm-30) REVERT: K 132 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7822 (mt-10) REVERT: K 155 LYS cc_start: 0.8303 (mppt) cc_final: 0.7913 (mmmt) REVERT: L 41 MET cc_start: 0.5843 (tmm) cc_final: 0.5558 (tmm) REVERT: L 43 TRP cc_start: 0.7648 (m-90) cc_final: 0.6530 (m-90) REVERT: L 59 LEU cc_start: 0.6279 (mm) cc_final: 0.4826 (pt) REVERT: L 82 TYR cc_start: 0.6748 (t80) cc_final: 0.6409 (m-10) REVERT: L 94 LEU cc_start: 0.8785 (pp) cc_final: 0.8284 (pp) REVERT: L 97 LEU cc_start: 0.8943 (tt) cc_final: 0.8468 (tt) outliers start: 3 outliers final: 2 residues processed: 385 average time/residue: 0.3441 time to fit residues: 184.4629 Evaluate side-chains 220 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 341 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN ** L 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16863 Z= 0.215 Angle : 0.629 8.147 22683 Z= 0.333 Chirality : 0.048 0.185 2537 Planarity : 0.004 0.050 2890 Dihedral : 5.120 53.817 2276 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.22 % Favored : 96.53 % Rotamer: Outliers : 1.68 % Allowed : 11.02 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2018 helix: 0.81 (0.20), residues: 616 sheet: -0.34 (0.21), residues: 549 loop : -0.56 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 122 HIS 0.008 0.001 HIS K 136 PHE 0.019 0.002 PHE J 199 TYR 0.017 0.002 TYR J 308 ARG 0.005 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 1.950 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: symmetry clash REVERT: A 126 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8582 (tm-30) REVERT: A 128 TYR cc_start: 0.8313 (t80) cc_final: 0.7988 (t80) REVERT: B 89 ARG cc_start: 0.7124 (mmm160) cc_final: 0.6902 (mmm160) REVERT: C 41 MET cc_start: 0.5937 (tmm) cc_final: 0.5327 (tmm) REVERT: C 42 PHE cc_start: 0.8077 (p90) cc_final: 0.7620 (p90) REVERT: C 43 TRP cc_start: 0.7643 (m-90) cc_final: 0.7071 (m-90) REVERT: C 102 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8928 (tm-30) REVERT: D 265 LEU cc_start: 0.8121 (tp) cc_final: 0.7844 (tp) REVERT: D 295 THR cc_start: 0.8267 (p) cc_final: 0.7758 (t) REVERT: E 181 MET cc_start: 0.6309 (mpp) cc_final: 0.5238 (ttm) REVERT: F 75 ASN cc_start: 0.7455 (m110) cc_final: 0.7140 (p0) REVERT: H 80 ASP cc_start: 0.8648 (t70) cc_final: 0.8309 (t0) REVERT: H 92 ASP cc_start: 0.7891 (m-30) cc_final: 0.7627 (m-30) REVERT: H 150 TYR cc_start: 0.8087 (m-10) cc_final: 0.7542 (m-10) REVERT: K 67 ASP cc_start: 0.7794 (t70) cc_final: 0.7461 (p0) REVERT: K 112 GLU cc_start: 0.7843 (tp30) cc_final: 0.7524 (mm-30) REVERT: K 132 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7775 (mt-10) REVERT: K 155 LYS cc_start: 0.8239 (mppt) cc_final: 0.7844 (mmmt) REVERT: L 43 TRP cc_start: 0.7670 (m-90) cc_final: 0.6969 (m-90) REVERT: L 82 TYR cc_start: 0.6998 (t80) cc_final: 0.6647 (m-10) outliers start: 30 outliers final: 21 residues processed: 266 average time/residue: 0.2967 time to fit residues: 115.2796 Evaluate side-chains 228 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 0.0040 chunk 50 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 163 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16863 Z= 0.188 Angle : 0.589 10.027 22683 Z= 0.307 Chirality : 0.047 0.174 2537 Planarity : 0.003 0.046 2890 Dihedral : 4.907 47.536 2274 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 2.07 % Allowed : 14.04 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2018 helix: 0.89 (0.20), residues: 616 sheet: -0.31 (0.21), residues: 551 loop : -0.58 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 117 HIS 0.007 0.001 HIS K 136 PHE 0.015 0.001 PHE J 252 TYR 0.016 0.001 TYR J 308 ARG 0.008 0.000 ARG I 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 2.025 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: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8316 (t80) cc_final: 0.8052 (t80) REVERT: B 80 ASP cc_start: 0.8381 (t0) cc_final: 0.8157 (t0) REVERT: C 20 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7528 (ptm160) REVERT: C 41 MET cc_start: 0.5859 (tmm) cc_final: 0.5313 (tmm) REVERT: C 42 PHE cc_start: 0.8136 (p90) cc_final: 0.7753 (p90) REVERT: C 43 TRP cc_start: 0.7654 (m-90) cc_final: 0.7020 (m-90) REVERT: C 58 ASP cc_start: 0.7984 (t0) cc_final: 0.7772 (t0) REVERT: D 265 LEU cc_start: 0.8159 (tp) cc_final: 0.7867 (tp) REVERT: D 295 THR cc_start: 0.8301 (p) cc_final: 0.7789 (t) REVERT: E 181 MET cc_start: 0.6281 (mpp) cc_final: 0.4967 (ttm) REVERT: F 39 ASP cc_start: 0.8619 (t0) cc_final: 0.8116 (p0) REVERT: F 75 ASN cc_start: 0.7463 (m110) cc_final: 0.7094 (p0) REVERT: G 271 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: G 305 ASP cc_start: 0.8146 (t0) cc_final: 0.7851 (t70) REVERT: I 117 TRP cc_start: 0.6858 (p90) cc_final: 0.6456 (p90) REVERT: K 67 ASP cc_start: 0.7778 (t70) cc_final: 0.7418 (p0) REVERT: K 103 TRP cc_start: 0.7852 (t60) cc_final: 0.7331 (t60) REVERT: K 155 LYS cc_start: 0.8232 (mppt) cc_final: 0.7853 (mmmt) REVERT: L 82 TYR cc_start: 0.6965 (t80) cc_final: 0.6734 (m-10) outliers start: 37 outliers final: 25 residues processed: 256 average time/residue: 0.2871 time to fit residues: 109.0855 Evaluate side-chains 227 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 GLN K 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16863 Z= 0.332 Angle : 0.652 9.382 22683 Z= 0.341 Chirality : 0.049 0.297 2537 Planarity : 0.004 0.045 2890 Dihedral : 5.070 48.983 2274 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.87 % Favored : 95.94 % Rotamer: Outliers : 3.30 % Allowed : 16.22 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2018 helix: 0.80 (0.21), residues: 619 sheet: -0.54 (0.21), residues: 561 loop : -0.71 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 117 HIS 0.006 0.002 HIS K 136 PHE 0.017 0.002 PHE A 252 TYR 0.015 0.002 TYR E 41 ARG 0.007 0.001 ARG J 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 214 time to evaluate : 1.951 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: A 79 ASN cc_start: 0.7928 (t0) cc_final: 0.7685 (t0) REVERT: B 121 MET cc_start: 0.8601 (tpp) cc_final: 0.8117 (tpp) REVERT: C 20 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7514 (ptm160) REVERT: C 89 PHE cc_start: 0.7036 (m-80) cc_final: 0.6798 (m-80) REVERT: D 265 LEU cc_start: 0.8161 (tp) cc_final: 0.7895 (tp) REVERT: D 295 THR cc_start: 0.8466 (p) cc_final: 0.7976 (t) REVERT: E 16 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8349 (mm) REVERT: E 181 MET cc_start: 0.6478 (mpp) cc_final: 0.5261 (ttm) REVERT: F 75 ASN cc_start: 0.7317 (m110) cc_final: 0.6886 (p0) REVERT: G 271 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: G 305 ASP cc_start: 0.8203 (t0) cc_final: 0.7844 (t70) REVERT: K 132 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7843 (mt-10) REVERT: K 155 LYS cc_start: 0.8168 (mppt) cc_final: 0.7698 (mmmt) outliers start: 59 outliers final: 38 residues processed: 253 average time/residue: 0.2543 time to fit residues: 99.1881 Evaluate side-chains 223 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 5 MET Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain L residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 0.3980 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 175 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16863 Z= 0.158 Angle : 0.580 14.354 22683 Z= 0.299 Chirality : 0.047 0.178 2537 Planarity : 0.003 0.045 2890 Dihedral : 4.788 48.668 2274 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 1.96 % Allowed : 19.02 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2018 helix: 0.96 (0.21), residues: 619 sheet: -0.41 (0.21), residues: 555 loop : -0.53 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 117 HIS 0.004 0.001 HIS K 125 PHE 0.022 0.001 PHE C 42 TYR 0.016 0.001 TYR J 308 ARG 0.003 0.000 ARG J 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 2.660 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: A 296 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7013 (ptpp) REVERT: A 320 ASN cc_start: 0.8230 (t0) cc_final: 0.7608 (t0) REVERT: B 121 MET cc_start: 0.8383 (tpp) cc_final: 0.7885 (tpp) REVERT: C 20 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7560 (ptm160) REVERT: C 89 PHE cc_start: 0.6836 (m-80) cc_final: 0.6582 (m-80) REVERT: D 265 LEU cc_start: 0.8143 (tp) cc_final: 0.7811 (tp) REVERT: D 295 THR cc_start: 0.8389 (p) cc_final: 0.7879 (t) REVERT: E 181 MET cc_start: 0.6454 (mpp) cc_final: 0.5113 (ttm) REVERT: F 75 ASN cc_start: 0.7340 (m110) cc_final: 0.6842 (p0) REVERT: F 105 ARG cc_start: 0.8648 (mtm110) cc_final: 0.8303 (mtm110) REVERT: G 271 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: K 103 TRP cc_start: 0.7885 (t60) cc_final: 0.7518 (t60) REVERT: K 132 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7850 (mt-10) REVERT: K 155 LYS cc_start: 0.8166 (mppt) cc_final: 0.7713 (mmmt) REVERT: L 37 LYS cc_start: 0.5645 (mmtp) cc_final: 0.5315 (mmtm) REVERT: L 43 TRP cc_start: 0.7736 (m-90) cc_final: 0.7134 (m-90) REVERT: L 80 HIS cc_start: 0.7754 (OUTLIER) cc_final: 0.6916 (m-70) outliers start: 35 outliers final: 21 residues processed: 236 average time/residue: 0.2734 time to fit residues: 97.4168 Evaluate side-chains 219 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain K residue 104 ARG Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 0.0070 chunk 195 optimal weight: 30.0000 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16863 Z= 0.288 Angle : 0.616 11.935 22683 Z= 0.321 Chirality : 0.048 0.180 2537 Planarity : 0.004 0.061 2890 Dihedral : 4.894 49.341 2274 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.04 % Rotamer: Outliers : 2.85 % Allowed : 19.30 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2018 helix: 0.92 (0.21), residues: 619 sheet: -0.52 (0.21), residues: 556 loop : -0.57 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 117 HIS 0.006 0.001 HIS B 136 PHE 0.013 0.002 PHE A 252 TYR 0.015 0.002 TYR A 70 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 ASN cc_start: 0.8369 (t0) cc_final: 0.7927 (t0) REVERT: B 121 MET cc_start: 0.8512 (tpp) cc_final: 0.8057 (tpp) REVERT: C 20 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7609 (ptm160) REVERT: C 89 PHE cc_start: 0.7002 (m-80) cc_final: 0.6736 (m-80) REVERT: D 265 LEU cc_start: 0.8166 (tp) cc_final: 0.7851 (tp) REVERT: D 295 THR cc_start: 0.8428 (p) cc_final: 0.7935 (t) REVERT: E 181 MET cc_start: 0.6588 (mpp) cc_final: 0.5213 (ttm) REVERT: F 75 ASN cc_start: 0.7253 (m110) cc_final: 0.6748 (p0) REVERT: F 102 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8404 (mt-10) REVERT: F 105 ARG cc_start: 0.8658 (mtm110) cc_final: 0.8223 (mtm110) REVERT: G 271 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: G 340 ASP cc_start: 0.7603 (t0) cc_final: 0.6131 (p0) REVERT: L 37 LYS cc_start: 0.5687 (mmtp) cc_final: 0.5399 (mmtm) REVERT: L 43 TRP cc_start: 0.7761 (m-90) cc_final: 0.7336 (m-90) REVERT: L 80 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6689 (m-70) outliers start: 51 outliers final: 39 residues processed: 237 average time/residue: 0.2660 time to fit residues: 97.2208 Evaluate side-chains 224 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 36 ASP Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 111 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16863 Z= 0.168 Angle : 0.581 10.925 22683 Z= 0.300 Chirality : 0.048 0.189 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.760 49.454 2274 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.53 % Favored : 97.27 % Rotamer: Outliers : 2.29 % Allowed : 20.86 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2018 helix: 0.95 (0.21), residues: 619 sheet: -0.35 (0.21), residues: 555 loop : -0.53 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 117 HIS 0.005 0.001 HIS B 136 PHE 0.018 0.001 PHE C 42 TYR 0.018 0.001 TYR G 227 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 208 time to evaluate : 1.894 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: A 56 ILE cc_start: 0.1953 (OUTLIER) cc_final: 0.1745 (tt) REVERT: A 162 ILE cc_start: 0.8813 (mm) cc_final: 0.8596 (mt) REVERT: A 296 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.6968 (ptpp) REVERT: A 320 ASN cc_start: 0.8326 (t0) cc_final: 0.7809 (t0) REVERT: B 121 MET cc_start: 0.8381 (tpp) cc_final: 0.7921 (tpp) REVERT: C 20 ARG cc_start: 0.8312 (mtp-110) cc_final: 0.7648 (ptm160) REVERT: C 89 PHE cc_start: 0.6879 (m-80) cc_final: 0.6603 (m-80) REVERT: D 265 LEU cc_start: 0.8162 (tp) cc_final: 0.7812 (tp) REVERT: D 295 THR cc_start: 0.8410 (p) cc_final: 0.7901 (t) REVERT: E 181 MET cc_start: 0.6544 (mpp) cc_final: 0.5102 (ttm) REVERT: F 75 ASN cc_start: 0.7224 (m110) cc_final: 0.6740 (p0) REVERT: F 105 ARG cc_start: 0.8644 (mtm110) cc_final: 0.8204 (mtm110) REVERT: G 243 GLN cc_start: 0.7896 (mm-40) cc_final: 0.6821 (pm20) REVERT: G 271 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7557 (pm20) REVERT: K 132 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7844 (mt-10) REVERT: K 155 LYS cc_start: 0.8072 (mppt) cc_final: 0.7578 (mmmt) REVERT: L 43 TRP cc_start: 0.7767 (m-90) cc_final: 0.7341 (m-90) outliers start: 41 outliers final: 30 residues processed: 236 average time/residue: 0.2783 time to fit residues: 99.1544 Evaluate side-chains 231 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 16863 Z= 0.161 Angle : 0.587 10.178 22683 Z= 0.300 Chirality : 0.047 0.170 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.683 49.165 2274 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.92 % Favored : 96.88 % Rotamer: Outliers : 2.52 % Allowed : 20.81 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 2018 helix: 1.25 (0.21), residues: 587 sheet: -0.32 (0.21), residues: 555 loop : -0.29 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP I 117 HIS 0.005 0.001 HIS E 125 PHE 0.014 0.001 PHE C 42 TYR 0.016 0.001 TYR G 227 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.0335 (tpt) cc_final: -0.1635 (mtt) REVERT: A 56 ILE cc_start: 0.1903 (OUTLIER) cc_final: 0.1658 (tt) REVERT: A 86 LYS cc_start: 0.8391 (pttt) cc_final: 0.8171 (pttp) REVERT: A 320 ASN cc_start: 0.8270 (t0) cc_final: 0.7788 (t0) REVERT: B 89 ARG cc_start: 0.7780 (mmm160) cc_final: 0.7456 (mmm160) REVERT: B 121 MET cc_start: 0.8389 (tpp) cc_final: 0.7929 (tpp) REVERT: C 20 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.7500 (ptm160) REVERT: C 89 PHE cc_start: 0.6920 (m-80) cc_final: 0.6660 (m-80) REVERT: D 265 LEU cc_start: 0.8165 (tp) cc_final: 0.7799 (tp) REVERT: D 283 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8761 (tm-30) REVERT: D 295 THR cc_start: 0.8417 (p) cc_final: 0.7908 (t) REVERT: D 301 LYS cc_start: 0.8982 (tptm) cc_final: 0.8684 (tptp) REVERT: E 181 MET cc_start: 0.6528 (mpp) cc_final: 0.5079 (ttm) REVERT: F 75 ASN cc_start: 0.7214 (m110) cc_final: 0.6739 (p0) REVERT: F 105 ARG cc_start: 0.8632 (mtm110) cc_final: 0.8193 (mtm110) REVERT: G 243 GLN cc_start: 0.7941 (mm-40) cc_final: 0.6910 (pm20) REVERT: G 271 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: J 247 MET cc_start: 0.4092 (ppp) cc_final: 0.3311 (ppp) REVERT: K 132 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7846 (mt-10) REVERT: L 43 TRP cc_start: 0.7787 (m-90) cc_final: 0.7369 (m-90) outliers start: 45 outliers final: 29 residues processed: 235 average time/residue: 0.2529 time to fit residues: 92.3268 Evaluate side-chains 226 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Chi-restraints excluded: chain L residue 68 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.0970 chunk 186 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 180 optimal weight: 0.0040 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16863 Z= 0.168 Angle : 0.603 10.487 22683 Z= 0.306 Chirality : 0.048 0.203 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.682 49.200 2274 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.97 % Favored : 96.83 % Rotamer: Outliers : 2.52 % Allowed : 21.03 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 2018 helix: 1.27 (0.21), residues: 587 sheet: -0.24 (0.21), residues: 578 loop : -0.29 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP I 117 HIS 0.005 0.001 HIS E 125 PHE 0.015 0.001 PHE L 89 TYR 0.016 0.001 TYR G 227 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.0647 (tpt) cc_final: -0.1388 (mtt) REVERT: A 56 ILE cc_start: 0.1907 (OUTLIER) cc_final: 0.1685 (tt) REVERT: A 86 LYS cc_start: 0.8440 (pttt) cc_final: 0.8204 (pttp) REVERT: A 320 ASN cc_start: 0.8260 (t0) cc_final: 0.7778 (t0) REVERT: B 16 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 89 ARG cc_start: 0.7726 (mmm160) cc_final: 0.7391 (mmm160) REVERT: B 121 MET cc_start: 0.8389 (tpp) cc_final: 0.7897 (tpp) REVERT: C 89 PHE cc_start: 0.6898 (m-80) cc_final: 0.6654 (m-80) REVERT: D 265 LEU cc_start: 0.8151 (tp) cc_final: 0.7789 (tp) REVERT: D 283 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8741 (tm-30) REVERT: D 295 THR cc_start: 0.8441 (p) cc_final: 0.7948 (t) REVERT: D 301 LYS cc_start: 0.8990 (tptm) cc_final: 0.8717 (tptp) REVERT: E 108 GLN cc_start: 0.8647 (mt0) cc_final: 0.8416 (mt0) REVERT: E 149 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: E 181 MET cc_start: 0.6528 (mpp) cc_final: 0.5090 (ttm) REVERT: F 75 ASN cc_start: 0.7260 (m110) cc_final: 0.6801 (p0) REVERT: F 105 ARG cc_start: 0.8614 (mtm110) cc_final: 0.8154 (mtm110) REVERT: G 243 GLN cc_start: 0.7905 (mm-40) cc_final: 0.6921 (pm20) REVERT: G 271 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: I 41 MET cc_start: 0.8516 (mmm) cc_final: 0.8236 (mmp) REVERT: K 132 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7840 (mt-10) REVERT: L 43 TRP cc_start: 0.7778 (m-90) cc_final: 0.7373 (m-90) outliers start: 45 outliers final: 31 residues processed: 239 average time/residue: 0.2545 time to fit residues: 94.1147 Evaluate side-chains 236 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 118 HIS Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.1980 chunk 191 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16863 Z= 0.172 Angle : 0.615 11.181 22683 Z= 0.312 Chirality : 0.047 0.200 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.696 49.304 2274 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.07 % Favored : 96.73 % Rotamer: Outliers : 2.24 % Allowed : 21.36 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2018 helix: 1.25 (0.21), residues: 587 sheet: -0.26 (0.21), residues: 578 loop : -0.31 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 117 HIS 0.005 0.001 HIS E 125 PHE 0.014 0.001 PHE C 42 TYR 0.018 0.001 TYR A 341 ARG 0.004 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4036 Ramachandran restraints generated. 2018 Oldfield, 0 Emsley, 2018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.0513 (tpt) cc_final: -0.1490 (mtt) REVERT: A 56 ILE cc_start: 0.1885 (OUTLIER) cc_final: 0.1646 (tt) REVERT: A 86 LYS cc_start: 0.8370 (pttt) cc_final: 0.8137 (pttp) REVERT: A 320 ASN cc_start: 0.8270 (t0) cc_final: 0.7757 (t0) REVERT: B 16 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8694 (mm) REVERT: B 89 ARG cc_start: 0.7745 (mmm160) cc_final: 0.7409 (mmm160) REVERT: B 121 MET cc_start: 0.8378 (tpp) cc_final: 0.7694 (tpp) REVERT: C 89 PHE cc_start: 0.6924 (m-80) cc_final: 0.6680 (m-80) REVERT: D 265 LEU cc_start: 0.8134 (tp) cc_final: 0.7773 (tp) REVERT: D 283 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8739 (tm-30) REVERT: D 295 THR cc_start: 0.8467 (p) cc_final: 0.7985 (t) REVERT: D 301 LYS cc_start: 0.8966 (tptm) cc_final: 0.8729 (tptp) REVERT: E 108 GLN cc_start: 0.8629 (mt0) cc_final: 0.8389 (mt0) REVERT: E 149 GLN cc_start: 0.8955 (pt0) cc_final: 0.8499 (tm-30) REVERT: E 181 MET cc_start: 0.6505 (mpp) cc_final: 0.5069 (ttm) REVERT: F 75 ASN cc_start: 0.7267 (m110) cc_final: 0.6862 (p0) REVERT: F 105 ARG cc_start: 0.8612 (mtm110) cc_final: 0.8371 (ptm-80) REVERT: G 243 GLN cc_start: 0.7950 (mm-40) cc_final: 0.6965 (pm20) REVERT: G 271 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: I 41 MET cc_start: 0.8495 (mmm) cc_final: 0.8175 (mmp) REVERT: K 132 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7845 (mt-10) REVERT: L 43 TRP cc_start: 0.7731 (m-90) cc_final: 0.7328 (m-90) outliers start: 40 outliers final: 32 residues processed: 236 average time/residue: 0.2523 time to fit residues: 91.6621 Evaluate side-chains 236 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 200 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 109 TYR Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 358 MET Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 271 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 118 HIS Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 249 ILE Chi-restraints excluded: chain K residue 97 ILE Chi-restraints excluded: chain L residue 40 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 4.9990 chunk 170 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.129035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.098244 restraints weight = 44788.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096473 restraints weight = 31332.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097372 restraints weight = 31051.583| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16863 Z= 0.209 Angle : 0.632 12.554 22683 Z= 0.322 Chirality : 0.048 0.273 2537 Planarity : 0.003 0.042 2890 Dihedral : 4.769 49.569 2274 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Rotamer: Outliers : 2.18 % Allowed : 21.81 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 2018 helix: 1.13 (0.21), residues: 587 sheet: -0.32 (0.21), residues: 581 loop : -0.31 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP I 117 HIS 0.005 0.001 HIS B 136 PHE 0.013 0.001 PHE J 252 TYR 0.029 0.001 TYR G 341 ARG 0.003 0.000 ARG I 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.77 seconds wall clock time: 57 minutes 37.24 seconds (3457.24 seconds total)