Starting phenix.real_space_refine on Sun Jun 30 18:16:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un0_42389/06_2024/8un0_42389_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un0_42389/06_2024/8un0_42389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un0_42389/06_2024/8un0_42389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un0_42389/06_2024/8un0_42389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un0_42389/06_2024/8un0_42389_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un0_42389/06_2024/8un0_42389_neut_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.068 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: 6 Type Number sf(0) Gaussians P 61 5.49 5 Mg 4 5.21 5 S 138 5.16 5 C 13599 2.51 5 N 3772 2.21 5 O 4286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 806": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "H GLU 256": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4319 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 512} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2591 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2541 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 315} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.84, per 1000 atoms: 0.54 Number of scatterers: 21860 At special positions: 0 Unit cell: (115.092, 129.168, 136.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 P 61 15.00 Mg 4 11.99 O 4286 8.00 N 3772 7.00 C 13599 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: 8.33 Conformation dependent library (CDL) restraints added in 3.1 seconds 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 17 sheets defined 43.2% alpha, 13.6% beta 17 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 8.80 Creating SS restraints... Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.950A pdb=" N TRP A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 406 through 417 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 496 through 503 removed outlier: 3.889A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 501 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 645 through 655 Processing helix chain 'A' and resid 667 through 688 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 698 through 708 Proline residue: A 702 - end of helix removed outlier: 3.595A pdb=" N LEU A 708 " --> pdb=" O PHE A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 742 Processing helix chain 'A' and resid 746 through 749 No H-bonds generated for 'chain 'A' and resid 746 through 749' Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 778 through 780 No H-bonds generated for 'chain 'A' and resid 778 through 780' Processing helix chain 'A' and resid 783 through 798 Processing helix chain 'A' and resid 838 through 862 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 82 through 101 Proline residue: B 96 - end of helix removed outlier: 5.618A pdb=" N LYS B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.717A pdb=" N ARG B 117 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.763A pdb=" N ARG B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.734A pdb=" N ARG B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 248 through 254 removed outlier: 4.015A pdb=" N VAL B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 removed outlier: 3.761A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 removed outlier: 3.596A pdb=" N LYS B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 348 removed outlier: 3.737A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.773A pdb=" N ARG C 139 " --> pdb=" O GLN C 135 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.527A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 277 through 290 removed outlier: 3.825A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 313 removed outlier: 4.212A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 339 removed outlier: 3.907A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 43 No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.721A pdb=" N ILE D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 104 No H-bonds generated for 'chain 'D' and resid 101 through 104' Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.855A pdb=" N VAL D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.768A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 224 through 234 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 265 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 286 through 298 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.693A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 97 through 116 removed outlier: 6.870A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP E 104 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG E 105 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU E 110 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET E 111 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU E 112 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS E 113 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 148 Processing helix chain 'E' and resid 151 through 154 No H-bonds generated for 'chain 'E' and resid 151 through 154' Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.687A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 209 through 218 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 308 through 324 Processing helix chain 'E' and resid 328 through 348 Processing helix chain 'F' and resid 9 through 16 removed outlier: 4.027A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.845A pdb=" N LYS F 77 " --> pdb=" O THR F 73 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 151 removed outlier: 3.502A pdb=" N ARG F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 215 No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'G' and resid 10 through 16 Processing helix chain 'G' and resid 141 through 154 removed outlier: 3.667A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.866A pdb=" N PHE G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 15 No H-bonds generated for 'chain 'H' and resid 12 through 15' Processing helix chain 'H' and resid 18 through 20 No H-bonds generated for 'chain 'H' and resid 18 through 20' Processing helix chain 'H' and resid 73 through 81 removed outlier: 3.898A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 153 removed outlier: 3.614A pdb=" N LEU H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 213 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing sheet with id= A, first strand: chain 'A' and resid 177 through 181 removed outlier: 3.516A pdb=" N VAL A 178 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 506 through 509 removed outlier: 7.222A pdb=" N ILE A 486 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU A 372 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N CYS A 488 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 396 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP A 435 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N MET A 398 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 803 through 807 removed outlier: 3.528A pdb=" N ILE A 814 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 186 through 189 removed outlier: 3.577A pdb=" N ILE B 73 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 170 through 174 removed outlier: 3.593A pdb=" N GLY C 60 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 195 through 199 removed outlier: 6.121A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 179 through 183 removed outlier: 6.404A pdb=" N HIS E 37 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL E 182 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 2 through 6 Processing sheet with id= I, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.837A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL F 237 " --> pdb=" O TYR F 249 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 204 through 208 removed outlier: 5.485A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE F 169 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 2 through 6 removed outlier: 3.560A pdb=" N ILE G 88 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.589A pdb=" N LEU G 66 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 237 " --> pdb=" O TYR G 249 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 203 through 208 removed outlier: 3.509A pdb=" N CYS G 162 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL G 167 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 2 through 5 removed outlier: 3.546A pdb=" N ALA H 4 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 26 through 29 Processing sheet with id= P, first strand: chain 'H' and resid 34 through 40 removed outlier: 3.732A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 203 through 208 removed outlier: 3.671A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) 882 hydrogen bonds defined for protein. 2529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 7.16 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7241 1.36 - 1.51: 5708 1.51 - 1.65: 9152 1.65 - 1.80: 99 1.80 - 1.95: 109 Bond restraints: 22309 Sorted by residual: bond pdb=" CA SER G 42 " pdb=" CB SER G 42 " ideal model delta sigma weight residual 1.529 1.457 0.073 1.63e-02 3.76e+03 1.99e+01 bond pdb=" N ASN B 272 " pdb=" CA ASN B 272 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.25e-02 6.40e+03 9.79e+00 bond pdb=" N MET G 75 " pdb=" CA MET G 75 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.26e-02 6.30e+03 9.35e+00 bond pdb=" N THR G 185 " pdb=" CA THR G 185 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.15e-02 7.56e+03 7.83e+00 bond pdb=" N ASN B 118 " pdb=" CA ASN B 118 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.37e-02 5.33e+03 7.68e+00 ... (remaining 22304 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.98: 759 105.98 - 113.49: 12485 113.49 - 121.01: 10662 121.01 - 128.53: 6351 128.53 - 136.05: 141 Bond angle restraints: 30398 Sorted by residual: angle pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" CD PRO A 535 " ideal model delta sigma weight residual 112.00 105.26 6.74 1.40e+00 5.10e-01 2.32e+01 angle pdb=" CA GLN E 119 " pdb=" CB GLN E 119 " pdb=" CG GLN E 119 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN A 363 " pdb=" CB GLN A 363 " pdb=" CG GLN A 363 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 angle pdb=" C SER G 183 " pdb=" N GLN G 184 " pdb=" CA GLN G 184 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" C PHE A 299 " ideal model delta sigma weight residual 110.97 106.19 4.78 1.09e+00 8.42e-01 1.93e+01 ... (remaining 30393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.73: 12380 26.73 - 53.45: 1106 53.45 - 80.18: 136 80.18 - 106.90: 11 106.90 - 133.62: 2 Dihedral angle restraints: 13635 sinusoidal: 5895 harmonic: 7740 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 166.38 133.62 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" CA SER H 183 " pdb=" C SER H 183 " pdb=" N GLN H 184 " pdb=" CA GLN H 184 " ideal model delta harmonic sigma weight residual 180.00 154.23 25.77 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA GLU G 109 " pdb=" C GLU G 109 " pdb=" N LYS G 110 " pdb=" CA LYS G 110 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 13632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3335 0.100 - 0.199: 194 0.199 - 0.299: 6 0.299 - 0.398: 0 0.398 - 0.498: 1 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE A 549 " pdb=" CA ILE A 549 " pdb=" CG1 ILE A 549 " pdb=" CG2 ILE A 549 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.20e+00 chirality pdb=" CA LEU E 93 " pdb=" N LEU E 93 " pdb=" C LEU E 93 " pdb=" CB LEU E 93 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE F 241 " pdb=" CA ILE F 241 " pdb=" CG1 ILE F 241 " pdb=" CG2 ILE F 241 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3533 not shown) Planarity restraints: 3723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU H 198 " 0.022 2.00e-02 2.50e+03 4.52e-02 2.05e+01 pdb=" C GLU H 198 " -0.078 2.00e-02 2.50e+03 pdb=" O GLU H 198 " 0.030 2.00e-02 2.50e+03 pdb=" N MET H 199 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A 699 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO E 174 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.053 5.00e-02 4.00e+02 ... (remaining 3720 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 248 2.63 - 3.20: 17625 3.20 - 3.77: 34885 3.77 - 4.33: 47167 4.33 - 4.90: 77928 Nonbonded interactions: 177853 Sorted by model distance: nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.069 2.170 nonbonded pdb=" OG1 THR D 85 " pdb="MG MG D 401 " model vdw 2.070 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2G AGS D 402 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR A 381 " pdb="MG MG A1201 " model vdw 2.075 2.170 ... (remaining 177848 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 'F' selection = (chain 'G' and resid 1 through 258) selection = (chain 'H' and resid 1 through 258) } 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: 1.940 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: 0.020 Extract box with map and model: 7.500 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 60.190 Find NCS groups from input model: 1.030 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: 0.010 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 0.083 22309 Z= 0.278 Angle : 0.803 12.645 30398 Z= 0.452 Chirality : 0.048 0.498 3536 Planarity : 0.007 0.108 3723 Dihedral : 18.780 133.625 8597 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.87 % Rotamer: Outliers : 0.56 % Allowed : 23.90 % Favored : 75.54 % 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: -1.93 (0.14), residues: 2623 helix: -1.49 (0.12), residues: 1195 sheet: -0.64 (0.22), residues: 519 loop : -1.03 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP F 28 HIS 0.010 0.001 HIS G 246 PHE 0.017 0.002 PHE G 169 TYR 0.016 0.002 TYR B 279 ARG 0.021 0.001 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 322 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 345 LYS cc_start: 0.8227 (ttpp) cc_final: 0.7975 (mppt) REVERT: F 149 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7444 (mmm-85) REVERT: H 117 LYS cc_start: 0.5768 (tptp) cc_final: 0.5457 (tptm) REVERT: H 199 MET cc_start: 0.3090 (mtm) cc_final: 0.2697 (mtp) outliers start: 13 outliers final: 1 residues processed: 329 average time/residue: 1.1675 time to fit residues: 442.6334 Evaluate side-chains 267 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.7980 chunk 200 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 125 optimal weight: 0.0470 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 40.0000 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 493 GLN A 573 GLN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN C 37 HIS C 241 HIS C 317 ASN D 308 ASN E 265 GLN F 71 ASN G 246 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22309 Z= 0.328 Angle : 0.611 8.358 30398 Z= 0.314 Chirality : 0.042 0.199 3536 Planarity : 0.005 0.084 3723 Dihedral : 14.388 134.883 3454 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.50 % Allowed : 24.11 % Favored : 71.39 % 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: -0.95 (0.16), residues: 2623 helix: -0.30 (0.14), residues: 1233 sheet: -0.60 (0.22), residues: 515 loop : -0.84 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 28 HIS 0.007 0.001 HIS C 289 PHE 0.017 0.002 PHE A 632 TYR 0.021 0.002 TYR F 250 ARG 0.013 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 276 time to evaluate : 2.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 102 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7590 (mtp180) REVERT: E 65 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: F 68 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8607 (mmt) REVERT: F 78 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8194 (mp) REVERT: F 88 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8157 (mp) REVERT: H 117 LYS cc_start: 0.5635 (tptp) cc_final: 0.5330 (tptm) REVERT: H 254 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6312 (mmmt) outliers start: 104 outliers final: 45 residues processed: 344 average time/residue: 1.1519 time to fit residues: 459.0448 Evaluate side-chains 296 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 245 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 240 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN E 320 HIS F 44 HIS F 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22309 Z= 0.315 Angle : 0.594 8.578 30398 Z= 0.304 Chirality : 0.042 0.194 3536 Planarity : 0.005 0.079 3723 Dihedral : 14.274 137.582 3453 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.24 % Allowed : 23.94 % Favored : 70.82 % 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: -0.47 (0.16), residues: 2623 helix: 0.18 (0.15), residues: 1228 sheet: -0.56 (0.22), residues: 528 loop : -0.59 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 28 HIS 0.007 0.001 HIS G 246 PHE 0.014 0.002 PHE A 558 TYR 0.015 0.002 TYR F 250 ARG 0.013 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 269 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7909 (mttt) REVERT: A 725 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: A 757 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 804 ARG cc_start: 0.7554 (ptm160) cc_final: 0.7309 (ptm160) REVERT: E 58 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6975 (tp30) REVERT: E 65 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: F 88 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8229 (mp) REVERT: F 199 MET cc_start: 0.5209 (ppp) cc_final: 0.4242 (pp-130) REVERT: G 72 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6941 (tt) REVERT: G 175 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6792 (mt) REVERT: G 197 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8062 (tp) REVERT: H 254 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6284 (mmmt) outliers start: 121 outliers final: 61 residues processed: 363 average time/residue: 1.1296 time to fit residues: 475.6186 Evaluate side-chains 308 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 237 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 306 LYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 228 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 724 GLN C 37 HIS D 219 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS G 38 GLN G 213 ASN G 246 HIS H 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22309 Z= 0.194 Angle : 0.536 7.209 30398 Z= 0.274 Chirality : 0.040 0.185 3536 Planarity : 0.004 0.074 3723 Dihedral : 14.088 143.684 3453 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.20 % Allowed : 26.19 % Favored : 69.61 % 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: -0.06 (0.17), residues: 2623 helix: 0.61 (0.15), residues: 1229 sheet: -0.57 (0.22), residues: 537 loop : -0.41 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 28 HIS 0.006 0.001 HIS G 246 PHE 0.022 0.001 PHE G 2 TYR 0.012 0.001 TYR B 42 ARG 0.013 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 269 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 299 PHE cc_start: 0.7493 (t80) cc_final: 0.6609 (t80) REVERT: A 757 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7639 (tp) REVERT: A 804 ARG cc_start: 0.7562 (ptm160) cc_final: 0.7320 (ptm160) REVERT: B 305 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8280 (t) REVERT: C 257 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7492 (mt0) REVERT: D 102 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7563 (mtp180) REVERT: E 58 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6838 (tp30) REVERT: E 65 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: F 42 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8166 (p) REVERT: G 25 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6210 (pm20) REVERT: G 72 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7020 (tt) REVERT: H 254 LYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6337 (mmmt) outliers start: 97 outliers final: 46 residues processed: 344 average time/residue: 1.1344 time to fit residues: 450.3753 Evaluate side-chains 297 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 241 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 190 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN C 37 HIS D 219 ASN E 72 GLN F 246 HIS G 246 HIS H 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22309 Z= 0.335 Angle : 0.613 8.552 30398 Z= 0.311 Chirality : 0.043 0.213 3536 Planarity : 0.005 0.076 3723 Dihedral : 14.208 150.057 3453 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.02 % Allowed : 25.19 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2623 helix: 0.54 (0.15), residues: 1229 sheet: -0.63 (0.22), residues: 547 loop : -0.41 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 28 HIS 0.007 0.001 HIS G 246 PHE 0.027 0.002 PHE G 2 TYR 0.018 0.002 TYR D 44 ARG 0.014 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 251 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: A 757 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7708 (tp) REVERT: A 804 ARG cc_start: 0.7593 (ptm160) cc_final: 0.7380 (ptm160) REVERT: D 102 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7624 (mtp180) REVERT: E 58 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: E 65 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: E 298 GLU cc_start: 0.8017 (tp30) cc_final: 0.7735 (tp30) REVERT: F 128 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5627 (mt) REVERT: F 199 MET cc_start: 0.5216 (ppp) cc_final: 0.4400 (pp-130) REVERT: G 25 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6384 (pm20) REVERT: G 175 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6819 (mt) REVERT: G 197 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8069 (tp) REVERT: H 19 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4422 (tm) REVERT: H 254 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6324 (mmmt) outliers start: 139 outliers final: 71 residues processed: 358 average time/residue: 1.1833 time to fit residues: 488.0606 Evaluate side-chains 321 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 240 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 214 PHE Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 254 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 21 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN C 37 HIS D 219 ASN E 71 HIS F 246 HIS G 36 ASN G 49 GLN ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN G 246 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22309 Z= 0.167 Angle : 0.547 8.449 30398 Z= 0.277 Chirality : 0.039 0.213 3536 Planarity : 0.004 0.073 3723 Dihedral : 14.048 152.748 3453 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.64 % Allowed : 27.88 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2623 helix: 0.90 (0.15), residues: 1229 sheet: -0.56 (0.22), residues: 539 loop : -0.34 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 28 HIS 0.009 0.001 HIS G 246 PHE 0.019 0.001 PHE G 2 TYR 0.010 0.001 TYR H 239 ARG 0.007 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 267 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7688 (tp) REVERT: A 805 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: C 320 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8355 (mm) REVERT: E 65 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: E 298 GLU cc_start: 0.7947 (tp30) cc_final: 0.7704 (tp30) REVERT: F 199 MET cc_start: 0.5057 (ppp) cc_final: 0.4317 (pp-130) REVERT: G 25 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.6214 (pm20) outliers start: 84 outliers final: 45 residues processed: 331 average time/residue: 1.2278 time to fit residues: 465.7498 Evaluate side-chains 293 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 243 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.1980 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 0.0470 chunk 186 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 40.0000 chunk 159 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN C 37 HIS D 219 ASN E 71 HIS F 246 HIS ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22309 Z= 0.177 Angle : 0.559 17.128 30398 Z= 0.280 Chirality : 0.039 0.182 3536 Planarity : 0.004 0.074 3723 Dihedral : 13.983 153.610 3453 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.77 % Allowed : 28.44 % Favored : 67.79 % 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: 0.36 (0.17), residues: 2623 helix: 1.04 (0.15), residues: 1231 sheet: -0.50 (0.22), residues: 544 loop : -0.24 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 28 HIS 0.007 0.001 HIS G 246 PHE 0.025 0.001 PHE G 2 TYR 0.016 0.001 TYR E 343 ARG 0.017 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 259 time to evaluate : 2.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (tp) REVERT: C 257 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: C 320 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8375 (mm) REVERT: E 65 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7241 (mm-30) REVERT: E 298 GLU cc_start: 0.8008 (tp30) cc_final: 0.7765 (tp30) REVERT: F 199 MET cc_start: 0.5064 (ppp) cc_final: 0.4203 (pp-130) REVERT: G 25 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6169 (pm20) REVERT: H 256 GLU cc_start: 0.5125 (pm20) cc_final: 0.3598 (pm20) outliers start: 87 outliers final: 54 residues processed: 330 average time/residue: 1.3287 time to fit residues: 507.4203 Evaluate side-chains 300 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 241 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 853 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 151 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 0.0060 chunk 125 optimal weight: 0.0040 chunk 23 optimal weight: 9.9990 chunk 200 optimal weight: 20.0000 chunk 231 optimal weight: 0.4980 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN A 564 GLN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 71 HIS E 72 GLN E 265 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22309 Z= 0.150 Angle : 0.548 14.713 30398 Z= 0.274 Chirality : 0.039 0.183 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.872 154.032 3453 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.81 % Allowed : 29.70 % Favored : 67.49 % 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: 0.56 (0.17), residues: 2623 helix: 1.21 (0.15), residues: 1229 sheet: -0.44 (0.22), residues: 542 loop : -0.10 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 28 HIS 0.007 0.000 HIS G 246 PHE 0.019 0.001 PHE G 2 TYR 0.021 0.001 TYR A 838 ARG 0.008 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 262 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 757 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 834 LYS cc_start: 0.8536 (tptt) cc_final: 0.8227 (tptt) REVERT: C 320 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8350 (mm) REVERT: E 298 GLU cc_start: 0.7990 (tp30) cc_final: 0.7769 (tp30) REVERT: F 199 MET cc_start: 0.5040 (ppp) cc_final: 0.4218 (pp-130) REVERT: G 25 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6160 (pm20) REVERT: G 68 MET cc_start: 0.5828 (tpt) cc_final: 0.5275 (tpt) REVERT: H 244 MET cc_start: -0.1598 (mtm) cc_final: -0.2322 (ptp) outliers start: 65 outliers final: 35 residues processed: 313 average time/residue: 1.2327 time to fit residues: 442.5113 Evaluate side-chains 289 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 251 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 20.0000 chunk 222 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS E 22 GLN E 265 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 22309 Z= 0.306 Angle : 0.624 13.525 30398 Z= 0.314 Chirality : 0.042 0.194 3536 Planarity : 0.005 0.083 3723 Dihedral : 14.035 154.536 3453 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.94 % Allowed : 30.00 % Favored : 67.06 % 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: 0.33 (0.17), residues: 2623 helix: 1.02 (0.15), residues: 1228 sheet: -0.54 (0.22), residues: 544 loop : -0.22 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 251 HIS 0.005 0.001 HIS C 289 PHE 0.021 0.002 PHE G 2 TYR 0.019 0.002 TYR B 42 ARG 0.025 0.001 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 245 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 320 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8419 (mm) REVERT: E 65 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: E 298 GLU cc_start: 0.8126 (tp30) cc_final: 0.7853 (tp30) REVERT: F 128 ILE cc_start: 0.5616 (OUTLIER) cc_final: 0.5412 (mt) REVERT: F 149 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7476 (mmm-85) REVERT: F 199 MET cc_start: 0.5227 (ppp) cc_final: 0.4300 (pp-130) REVERT: F 240 LYS cc_start: 0.8285 (tppt) cc_final: 0.8067 (tppt) REVERT: G 25 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6239 (pm20) REVERT: H 40 MET cc_start: 0.4120 (mtm) cc_final: 0.3801 (mtp) outliers start: 68 outliers final: 46 residues processed: 305 average time/residue: 1.2431 time to fit residues: 434.3387 Evaluate side-chains 289 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 161 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 chunk 242 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 547 ASN ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN E 22 GLN E 72 GLN G 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22309 Z= 0.173 Angle : 0.570 13.471 30398 Z= 0.285 Chirality : 0.039 0.191 3536 Planarity : 0.004 0.072 3723 Dihedral : 13.929 155.763 3453 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.12 % Allowed : 31.13 % Favored : 66.75 % 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: 0.50 (0.17), residues: 2623 helix: 1.15 (0.15), residues: 1240 sheet: -0.47 (0.22), residues: 539 loop : -0.15 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.006 0.001 HIS G 246 PHE 0.021 0.001 PHE G 169 TYR 0.018 0.001 TYR A 838 ARG 0.007 0.000 ARG F 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5246 Ramachandran restraints generated. 2623 Oldfield, 0 Emsley, 2623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 248 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 320 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8358 (mm) REVERT: F 199 MET cc_start: 0.5104 (ppp) cc_final: 0.4307 (pp-130) REVERT: F 240 LYS cc_start: 0.8302 (tppt) cc_final: 0.8086 (tppt) REVERT: G 25 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6155 (pm20) REVERT: H 40 MET cc_start: 0.4100 (mtm) cc_final: 0.3465 (mtp) outliers start: 49 outliers final: 39 residues processed: 288 average time/residue: 1.2515 time to fit residues: 411.9947 Evaluate side-chains 284 residues out of total 2312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 180 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 30 optimal weight: 0.0170 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 72 GLN E 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.175077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.129981 restraints weight = 28540.594| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.61 r_work: 0.3388 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22309 Z= 0.173 Angle : 0.568 13.273 30398 Z= 0.284 Chirality : 0.039 0.197 3536 Planarity : 0.004 0.076 3723 Dihedral : 13.876 155.584 3453 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.16 % Allowed : 31.30 % Favored : 66.54 % 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: 0.59 (0.17), residues: 2623 helix: 1.22 (0.15), residues: 1240 sheet: -0.41 (0.22), residues: 545 loop : -0.11 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.006 0.001 HIS B 259 PHE 0.020 0.001 PHE G 169 TYR 0.017 0.001 TYR A 838 ARG 0.024 0.000 ARG C 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7786.99 seconds wall clock time: 136 minutes 48.19 seconds (8208.19 seconds total)