Starting phenix.real_space_refine on Thu Mar 14 19:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ic0_35351/03_2024/8ic0_35351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ic0_35351/03_2024/8ic0_35351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ic0_35351/03_2024/8ic0_35351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ic0_35351/03_2024/8ic0_35351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ic0_35351/03_2024/8ic0_35351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ic0_35351/03_2024/8ic0_35351.pdb" } resolution = 3.41 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= 0.005 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 6100 2.51 5 N 1638 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9553 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2420 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 564 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Time building chain proxies: 5.44, per 1000 atoms: 0.57 Number of scatterers: 9553 At special positions: 0 Unit cell: (91.216, 122.337, 149.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1744 8.00 N 1638 7.00 C 6100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 34 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 50 " distance=2.03 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: 3.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 35 through 68 removed outlier: 3.521A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 102 removed outlier: 3.980A pdb=" N VAL A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.858A pdb=" N SER A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 140 removed outlier: 3.585A pdb=" N LYS A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.582A pdb=" N ASN A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.830A pdb=" N PHE A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.892A pdb=" N VAL A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.760A pdb=" N HIS A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 3.594A pdb=" N PHE A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 270 removed outlier: 3.692A pdb=" N ILE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.645A pdb=" N THR A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.579A pdb=" N ASN A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 4.476A pdb=" N ILE A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.674A pdb=" N HIS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 removed outlier: 4.600A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.676A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.273A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.957A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.522A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.784A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 352 removed outlier: 4.236A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 4.070A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.883A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.526A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.842A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.709A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.703A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.895A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.517A pdb=" N GLN F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 61 " --> pdb=" O TRP F 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 186 removed outlier: 3.906A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.163A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.957A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.378A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 149 through 153 removed outlier: 6.613A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.724A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.688A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.507A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.365A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.622A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.528A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 178 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 28 removed outlier: 4.475A pdb=" N GLU F 24 " --> pdb=" O LYS F 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS F 42 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 38 " --> pdb=" O ILE F 28 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 3.66 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: 3081 1.34 - 1.46: 2281 1.46 - 1.58: 4289 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9752 Sorted by residual: bond pdb=" CB PRO A 180 " pdb=" CG PRO A 180 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.46e+00 bond pdb=" CA PHE A 174 " pdb=" CB PHE A 174 " ideal model delta sigma weight residual 1.528 1.569 -0.040 2.61e-02 1.47e+03 2.38e+00 bond pdb=" C ASP C 333 " pdb=" N SER C 334 " ideal model delta sigma weight residual 1.332 1.312 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.35e+00 bond pdb=" CA ILE A 139 " pdb=" CB ILE A 139 " ideal model delta sigma weight residual 1.545 1.535 0.010 9.10e-03 1.21e+04 1.32e+00 ... (remaining 9747 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.26: 136 105.26 - 112.44: 5025 112.44 - 119.63: 3189 119.63 - 126.81: 4733 126.81 - 134.00: 126 Bond angle restraints: 13209 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 107.78 5.93 9.50e-01 1.11e+00 3.89e+01 angle pdb=" N ILE C 33 " pdb=" CA ILE C 33 " pdb=" C ILE C 33 " ideal model delta sigma weight residual 113.42 108.77 4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" N VAL A 272 " pdb=" CA VAL A 272 " pdb=" C VAL A 272 " ideal model delta sigma weight residual 111.56 108.59 2.97 8.60e-01 1.35e+00 1.19e+01 angle pdb=" C ASP C 118 " pdb=" N ASN C 119 " pdb=" CA ASN C 119 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 115.75 5.79 1.91e+00 2.74e-01 9.19e+00 ... (remaining 13204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5225 17.54 - 35.08: 479 35.08 - 52.62: 87 52.62 - 70.16: 11 70.16 - 87.69: 7 Dihedral angle restraints: 5809 sinusoidal: 2247 harmonic: 3562 Sorted by residual: dihedral pdb=" CA TYR E 178 " pdb=" C TYR E 178 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " ideal model delta harmonic sigma weight residual -180.00 -144.01 -35.99 0 5.00e+00 4.00e-02 5.18e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -131.34 45.34 1 1.00e+01 1.00e-02 2.85e+01 ... (remaining 5806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 960 0.032 - 0.064: 392 0.064 - 0.096: 89 0.096 - 0.127: 66 0.127 - 0.159: 4 Chirality restraints: 1511 Sorted by residual: chirality pdb=" CA ASN C 119 " pdb=" N ASN C 119 " pdb=" C ASN C 119 " pdb=" CB ASN C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA TRP C 332 " pdb=" N TRP C 332 " pdb=" C TRP C 332 " pdb=" CB TRP C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1508 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 179 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 180 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " 0.018 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP C 332 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 194 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.027 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 9590 3.26 - 3.81: 14494 3.81 - 4.35: 18741 4.35 - 4.90: 31644 Nonbonded interactions: 74757 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.163 2.440 nonbonded pdb=" OE1 GLN E 130 " pdb=" OG1 THR E 231 " model vdw 2.198 2.440 nonbonded pdb=" OG SER E 192 " pdb=" OG1 THR E 203 " model vdw 2.284 2.440 nonbonded pdb=" OH TYR E 101 " pdb=" NE2 HIS E 220 " model vdw 2.292 2.520 nonbonded pdb=" OH TYR C 289 " pdb=" NE1 TRP C 297 " model vdw 2.300 2.520 ... (remaining 74752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.200 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.180 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 : 0.003 0.078 9752 Z= 0.199 Angle : 0.550 6.760 13209 Z= 0.296 Chirality : 0.041 0.159 1511 Planarity : 0.004 0.104 1665 Dihedral : 13.845 87.694 3491 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1212 helix: 0.04 (0.27), residues: 373 sheet: -1.48 (0.34), residues: 258 loop : -1.49 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 332 HIS 0.006 0.001 HIS B 188 PHE 0.020 0.001 PHE A 174 TYR 0.025 0.001 TYR E 178 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.6706 (tpp) cc_final: 0.6252 (ttm) REVERT: C 61 MET cc_start: 0.7823 (ppp) cc_final: 0.7478 (ppp) REVERT: E 13 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7871 (mm110) REVERT: E 77 ASN cc_start: 0.7464 (t0) cc_final: 0.7260 (t0) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2072 time to fit residues: 40.3604 Evaluate side-chains 110 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 271 GLN A 311 ASN B 244 HIS B 331 ASN C 220 GLN C 259 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9752 Z= 0.234 Angle : 0.579 7.341 13209 Z= 0.300 Chirality : 0.042 0.135 1511 Planarity : 0.004 0.066 1665 Dihedral : 4.312 34.467 1327 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.97 % Allowed : 9.15 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1212 helix: 0.75 (0.26), residues: 379 sheet: -1.45 (0.33), residues: 266 loop : -1.34 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 332 HIS 0.004 0.001 HIS B 188 PHE 0.018 0.001 PHE A 174 TYR 0.027 0.001 TYR E 178 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.063 Fit side-chains REVERT: B 53 MET cc_start: 0.6498 (tpp) cc_final: 0.6261 (ttm) REVERT: C 61 MET cc_start: 0.7979 (ppp) cc_final: 0.7650 (ppp) REVERT: D 42 GLU cc_start: 0.8343 (pp20) cc_final: 0.8116 (mm-30) REVERT: E 13 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7833 (mm110) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.2111 time to fit residues: 36.8905 Evaluate side-chains 118 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 0.0870 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN B 333 GLN C 266 HIS ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9752 Z= 0.241 Angle : 0.556 5.892 13209 Z= 0.286 Chirality : 0.042 0.134 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.303 34.444 1327 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.36 % Allowed : 13.05 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1212 helix: 0.93 (0.26), residues: 380 sheet: -1.49 (0.33), residues: 260 loop : -1.38 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 332 HIS 0.007 0.001 HIS B 188 PHE 0.015 0.001 PHE A 174 TYR 0.026 0.001 TYR E 178 ARG 0.007 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.063 Fit side-chains REVERT: B 53 MET cc_start: 0.6540 (tpp) cc_final: 0.6324 (ttm) REVERT: C 61 MET cc_start: 0.8018 (ppp) cc_final: 0.7812 (ppp) REVERT: C 188 MET cc_start: 0.7113 (mtt) cc_final: 0.6354 (mtt) REVERT: C 220 GLN cc_start: 0.8358 (mt0) cc_final: 0.8043 (mt0) REVERT: C 325 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6638 (mtt) REVERT: E 13 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7744 (mm110) outliers start: 14 outliers final: 9 residues processed: 123 average time/residue: 0.2053 time to fit residues: 36.0095 Evaluate side-chains 119 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9752 Z= 0.313 Angle : 0.584 7.576 13209 Z= 0.300 Chirality : 0.043 0.140 1511 Planarity : 0.004 0.054 1665 Dihedral : 4.424 33.787 1327 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.75 % Allowed : 15.29 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1212 helix: 0.94 (0.27), residues: 380 sheet: -1.44 (0.32), residues: 273 loop : -1.41 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.009 0.001 HIS C 266 PHE 0.016 0.001 PHE E 27 TYR 0.026 0.002 TYR E 178 ARG 0.006 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.081 Fit side-chains REVERT: C 61 MET cc_start: 0.8197 (ppp) cc_final: 0.7989 (ppp) REVERT: C 188 MET cc_start: 0.7163 (mtt) cc_final: 0.6553 (mtt) REVERT: C 220 GLN cc_start: 0.8416 (mt0) cc_final: 0.8028 (mt0) REVERT: C 234 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.6906 (t80) outliers start: 18 outliers final: 9 residues processed: 118 average time/residue: 0.2174 time to fit residues: 36.7741 Evaluate side-chains 111 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 98 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 60.0000 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9752 Z= 0.262 Angle : 0.559 7.360 13209 Z= 0.286 Chirality : 0.042 0.138 1511 Planarity : 0.004 0.053 1665 Dihedral : 4.372 34.086 1327 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.53 % Allowed : 16.85 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1212 helix: 0.98 (0.27), residues: 381 sheet: -1.52 (0.31), residues: 285 loop : -1.41 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 121 TYR 0.023 0.001 TYR E 178 ARG 0.004 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.090 Fit side-chains REVERT: A 165 MET cc_start: 0.5297 (mmt) cc_final: 0.4157 (mtp) REVERT: C 188 MET cc_start: 0.7163 (mtt) cc_final: 0.6512 (mtt) REVERT: C 220 GLN cc_start: 0.8427 (mt0) cc_final: 0.8073 (mt0) REVERT: C 234 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.6805 (t80) outliers start: 26 outliers final: 17 residues processed: 129 average time/residue: 0.2018 time to fit residues: 37.4941 Evaluate side-chains 124 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 116 optimal weight: 50.0000 chunk 96 optimal weight: 0.0270 chunk 53 optimal weight: 30.0000 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9752 Z= 0.147 Angle : 0.517 7.925 13209 Z= 0.262 Chirality : 0.040 0.130 1511 Planarity : 0.003 0.051 1665 Dihedral : 4.122 33.891 1327 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.04 % Allowed : 17.82 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.24), residues: 1212 helix: 1.19 (0.27), residues: 383 sheet: -1.32 (0.32), residues: 283 loop : -1.41 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 121 TYR 0.020 0.001 TYR E 178 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.061 Fit side-chains REVERT: A 165 MET cc_start: 0.5155 (mmt) cc_final: 0.4038 (mtp) REVERT: C 188 MET cc_start: 0.7121 (mtt) cc_final: 0.6410 (mtt) REVERT: C 220 GLN cc_start: 0.8427 (mt0) cc_final: 0.8023 (mt0) REVERT: C 234 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.6976 (t80) REVERT: E 221 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8233 (tt) outliers start: 21 outliers final: 12 residues processed: 130 average time/residue: 0.1932 time to fit residues: 36.4020 Evaluate side-chains 123 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS B 213 HIS B 331 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9752 Z= 0.261 Angle : 0.566 7.544 13209 Z= 0.288 Chirality : 0.041 0.166 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.261 33.293 1327 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.92 % Allowed : 17.92 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1212 helix: 1.16 (0.27), residues: 383 sheet: -1.50 (0.31), residues: 285 loop : -1.44 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 211 HIS 0.006 0.001 HIS B 188 PHE 0.015 0.001 PHE A 121 TYR 0.024 0.001 TYR E 178 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.052 Fit side-chains REVERT: A 165 MET cc_start: 0.4987 (mmt) cc_final: 0.3894 (mtp) REVERT: C 75 GLN cc_start: 0.7260 (mt0) cc_final: 0.7048 (mt0) REVERT: C 117 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8074 (tp) REVERT: C 188 MET cc_start: 0.7227 (mtt) cc_final: 0.6579 (mtt) REVERT: C 220 GLN cc_start: 0.8508 (mt0) cc_final: 0.8124 (mt0) REVERT: C 234 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.6649 (t80) REVERT: E 221 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (tt) outliers start: 30 outliers final: 21 residues processed: 133 average time/residue: 0.1863 time to fit residues: 36.2585 Evaluate side-chains 132 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 0.0970 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 239 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9752 Z= 0.171 Angle : 0.538 8.677 13209 Z= 0.270 Chirality : 0.040 0.155 1511 Planarity : 0.003 0.051 1665 Dihedral : 4.152 33.828 1327 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.53 % Allowed : 18.70 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.86 (0.24), residues: 1212 helix: 1.26 (0.27), residues: 383 sheet: -1.41 (0.31), residues: 280 loop : -1.40 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.004 0.001 HIS B 188 PHE 0.010 0.001 PHE E 27 TYR 0.021 0.001 TYR E 178 ARG 0.001 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.063 Fit side-chains REVERT: A 165 MET cc_start: 0.5019 (mmt) cc_final: 0.3943 (mtp) REVERT: C 188 MET cc_start: 0.7341 (mtt) cc_final: 0.6596 (mtt) REVERT: C 220 GLN cc_start: 0.8486 (mt0) cc_final: 0.8108 (mt0) REVERT: C 234 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.6621 (t80) REVERT: E 221 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (tt) outliers start: 26 outliers final: 17 residues processed: 131 average time/residue: 0.1811 time to fit residues: 34.6137 Evaluate side-chains 128 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 0.0060 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 75 GLN C 220 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9752 Z= 0.155 Angle : 0.535 8.692 13209 Z= 0.268 Chirality : 0.040 0.150 1511 Planarity : 0.003 0.051 1665 Dihedral : 4.084 34.288 1327 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.85 % Allowed : 19.18 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.78 (0.25), residues: 1212 helix: 1.38 (0.27), residues: 383 sheet: -1.36 (0.31), residues: 289 loop : -1.40 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.006 0.001 HIS B 188 PHE 0.010 0.001 PHE E 27 TYR 0.022 0.001 TYR E 178 ARG 0.002 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.115 Fit side-chains REVERT: A 165 MET cc_start: 0.4994 (mmt) cc_final: 0.3927 (mtp) REVERT: C 188 MET cc_start: 0.7327 (mtt) cc_final: 0.6586 (mtt) REVERT: C 220 GLN cc_start: 0.8401 (mt0) cc_final: 0.8049 (mt0) REVERT: C 234 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.6700 (t80) REVERT: E 218 MET cc_start: 0.7360 (ttt) cc_final: 0.7089 (ttt) outliers start: 19 outliers final: 17 residues processed: 131 average time/residue: 0.1917 time to fit residues: 36.8918 Evaluate side-chains 126 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 50.0000 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 75 GLN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9752 Z= 0.191 Angle : 0.553 8.569 13209 Z= 0.276 Chirality : 0.040 0.147 1511 Planarity : 0.003 0.050 1665 Dihedral : 4.128 35.698 1327 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.95 % Allowed : 19.47 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.80 (0.24), residues: 1212 helix: 1.38 (0.27), residues: 383 sheet: -1.38 (0.31), residues: 289 loop : -1.42 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 211 HIS 0.005 0.001 HIS B 188 PHE 0.011 0.001 PHE E 27 TYR 0.026 0.001 TYR E 178 ARG 0.002 0.000 ARG A 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.048 Fit side-chains REVERT: A 165 MET cc_start: 0.5147 (mmt) cc_final: 0.3936 (mtp) REVERT: A 241 MET cc_start: 0.7578 (ttt) cc_final: 0.7210 (ttp) REVERT: C 188 MET cc_start: 0.7366 (mtt) cc_final: 0.6628 (mtt) REVERT: C 220 GLN cc_start: 0.8403 (mt0) cc_final: 0.8073 (mt0) REVERT: C 234 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.6662 (t80) outliers start: 20 outliers final: 19 residues processed: 125 average time/residue: 0.1969 time to fit residues: 35.5119 Evaluate side-chains 127 residues out of total 1059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain B residue 311 ASN Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 97 optimal weight: 0.0770 chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.194798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127482 restraints weight = 11430.298| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.47 r_work: 0.3324 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9752 Z= 0.142 Angle : 0.543 9.039 13209 Z= 0.269 Chirality : 0.040 0.145 1511 Planarity : 0.003 0.050 1665 Dihedral : 4.032 35.660 1327 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.95 % Allowed : 19.38 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.73 (0.25), residues: 1212 helix: 1.52 (0.27), residues: 383 sheet: -1.29 (0.31), residues: 289 loop : -1.48 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.004 0.000 HIS B 188 PHE 0.009 0.001 PHE E 27 TYR 0.023 0.001 TYR E 178 ARG 0.002 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2086.11 seconds wall clock time: 38 minutes 23.51 seconds (2303.51 seconds total)