Starting phenix.real_space_refine on Tue Nov 21 02:08:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/11_2023/8c5z_16445.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/11_2023/8c5z_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_16445/11_2023/8c5z_16445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/11_2023/8c5z_16445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/11_2023/8c5z_16445.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5z_16445/11_2023/8c5z_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-1.21rc1-5144/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: 8.95, per 1000 atoms: 0.54 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: 6.06 Conformation dependent library (CDL) restraints added in 2.9 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: 1.93 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: 4.78 Time building geometry restraints manager: 6.56 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 12.500 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 45.600 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.610 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.976 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 outliers start: 3 outliers final: 2 residues processed: 385 average time/residue: 0.3500 time to fit residues: 188.1581 Evaluate side-chains 207 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1774 time to fit residues: 3.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 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 ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16863 Z= 0.222 Angle : 0.648 8.809 22683 Z= 0.342 Chirality : 0.048 0.183 2537 Planarity : 0.004 0.059 2890 Dihedral : 5.047 54.400 2273 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.17 % Favored : 96.58 % Rotamer: Outliers : 1.79 % Allowed : 11.41 % Favored : 86.80 % 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: -0.19 (0.18), residues: 2018 helix: 0.80 (0.20), residues: 615 sheet: -0.32 (0.21), residues: 550 loop : -0.54 (0.21), residues: 853 *********************** 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 268 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 1.871 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 outliers start: 32 outliers final: 21 residues processed: 255 average time/residue: 0.3033 time to fit residues: 113.1668 Evaluate side-chains 216 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1627 time to fit residues: 8.8490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 0.0010 chunk 50 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7129 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16863 Z= 0.195 Angle : 0.601 10.021 22683 Z= 0.314 Chirality : 0.047 0.173 2537 Planarity : 0.004 0.046 2890 Dihedral : 4.894 48.429 2273 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 1.23 % Allowed : 14.04 % Favored : 84.73 % 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: -0.17 (0.18), residues: 2018 helix: 0.86 (0.20), residues: 616 sheet: -0.29 (0.21), residues: 543 loop : -0.59 (0.21), residues: 859 *********************** 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 253 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 2.173 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 outliers start: 22 outliers final: 7 residues processed: 244 average time/residue: 0.2975 time to fit residues: 108.1030 Evaluate side-chains 203 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2008 time to fit residues: 4.9785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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** ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16863 Z= 0.285 Angle : 0.627 13.056 22683 Z= 0.327 Chirality : 0.048 0.224 2537 Planarity : 0.004 0.045 2890 Dihedral : 4.910 48.563 2273 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.37 % Favored : 96.43 % Rotamer: Outliers : 1.51 % Allowed : 17.17 % Favored : 81.32 % 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: -0.28 (0.18), residues: 2018 helix: 0.82 (0.20), residues: 619 sheet: -0.44 (0.21), residues: 545 loop : -0.62 (0.21), residues: 854 *********************** 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 234 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 1.952 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 outliers start: 27 outliers final: 14 residues processed: 220 average time/residue: 0.2751 time to fit residues: 92.7701 Evaluate side-chains 199 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1561 time to fit residues: 6.8039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 134 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 99 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 162 ASN ** 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: 0.7141 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16863 Z= 0.172 Angle : 0.587 11.084 22683 Z= 0.304 Chirality : 0.047 0.165 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.768 48.571 2273 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.92 % Favored : 96.88 % Rotamer: Outliers : 1.40 % Allowed : 18.62 % Favored : 79.98 % 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: 0.05 (0.19), residues: 2018 helix: 1.21 (0.21), residues: 587 sheet: -0.38 (0.22), residues: 511 loop : -0.37 (0.21), residues: 920 *********************** 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 244 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 1.868 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 outliers start: 25 outliers final: 7 residues processed: 237 average time/residue: 0.2825 time to fit residues: 101.5873 Evaluate side-chains 202 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1606 time to fit residues: 4.9878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16863 Z= 0.207 Angle : 0.601 10.411 22683 Z= 0.309 Chirality : 0.047 0.166 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.830 55.717 2273 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.02 % Favored : 96.78 % Rotamer: Outliers : 1.40 % Allowed : 19.91 % Favored : 78.69 % 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 (0.19), residues: 2018 helix: 1.27 (0.21), residues: 587 sheet: -0.34 (0.21), residues: 556 loop : -0.37 (0.22), residues: 875 *********************** 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 232 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 225 average time/residue: 0.2551 time to fit residues: 89.5955 Evaluate side-chains 206 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1695 time to fit residues: 7.2251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 109 optimal weight: 0.0970 chunk 194 optimal weight: 9.9990 chunk 121 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16863 Z= 0.167 Angle : 0.590 9.621 22683 Z= 0.302 Chirality : 0.048 0.200 2537 Planarity : 0.003 0.045 2890 Dihedral : 4.747 51.701 2273 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.78 % Favored : 97.03 % Rotamer: Outliers : 1.06 % Allowed : 20.25 % Favored : 78.69 % 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: -0.25 (0.22), residues: 523 loop : -0.33 (0.21), residues: 908 *********************** 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 230 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 211 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 224 average time/residue: 0.2617 time to fit residues: 91.2718 Evaluate side-chains 201 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1646 time to fit residues: 4.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 132 optimal weight: 0.0570 chunk 96 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16863 Z= 0.156 Angle : 0.607 11.492 22683 Z= 0.305 Chirality : 0.047 0.164 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.683 52.835 2273 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 1.17 % Allowed : 20.36 % Favored : 78.47 % 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 (0.19), residues: 2018 helix: 1.27 (0.21), residues: 587 sheet: -0.17 (0.22), residues: 523 loop : -0.28 (0.21), residues: 908 *********************** 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 233 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 227 average time/residue: 0.2635 time to fit residues: 92.2265 Evaluate side-chains 204 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 1.942 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1567 time to fit residues: 4.3595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.8980 chunk 186 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 109 optimal weight: 0.0570 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16863 Z= 0.169 Angle : 0.611 10.079 22683 Z= 0.309 Chirality : 0.047 0.204 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.700 49.127 2273 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.78 % Favored : 97.03 % Rotamer: Outliers : 0.50 % Allowed : 21.14 % Favored : 78.36 % 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: 0.25 (0.19), residues: 2018 helix: 1.30 (0.21), residues: 587 sheet: -0.19 (0.22), residues: 526 loop : -0.25 (0.22), residues: 905 *********************** 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 218 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 209 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 213 average time/residue: 0.2572 time to fit residues: 85.8039 Evaluate side-chains 194 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1481 time to fit residues: 3.4344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 185 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 16 optimal weight: 0.0270 chunk 123 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16863 Z= 0.167 Angle : 0.628 11.280 22683 Z= 0.315 Chirality : 0.047 0.176 2537 Planarity : 0.003 0.044 2890 Dihedral : 4.690 49.197 2273 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.98 % Rotamer: Outliers : 0.22 % Allowed : 21.36 % Favored : 78.41 % 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 (0.19), residues: 2018 helix: 1.28 (0.21), residues: 587 sheet: -0.27 (0.22), residues: 541 loop : -0.22 (0.22), residues: 890 ********************** 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 211 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 211 average time/residue: 0.2598 time to fit residues: 87.8946 Evaluate side-chains 198 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 160 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 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 = 0.4126 r_free = 0.4126 target = 0.130888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.099808 restraints weight = 44826.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.098152 restraints weight = 30666.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.099517 restraints weight = 29101.592| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16863 Z= 0.169 Angle : 0.632 15.234 22683 Z= 0.317 Chirality : 0.047 0.190 2537 Planarity : 0.003 0.043 2890 Dihedral : 4.689 49.325 2273 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.73 % Favored : 97.08 % Rotamer: Outliers : 0.34 % Allowed : 21.81 % 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: 0.22 (0.19), residues: 2018 helix: 1.21 (0.21), residues: 596 sheet: -0.25 (0.21), residues: 565 loop : -0.19 (0.22), residues: 857 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.42 seconds wall clock time: 58 minutes 53.48 seconds (3533.48 seconds total)