Starting phenix.real_space_refine on Sun Aug 24 07:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw8_41662/08_2025/8tw8_41662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw8_41662/08_2025/8tw8_41662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw8_41662/08_2025/8tw8_41662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw8_41662/08_2025/8tw8_41662.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw8_41662/08_2025/8tw8_41662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw8_41662/08_2025/8tw8_41662.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.008 sd= 0.057 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 11 5.49 5 Mg 3 5.21 5 S 83 5.16 5 C 11632 2.51 5 N 3112 2.21 5 O 3578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18419 Number of models: 1 Model: "" Number of chains: 12 Chain: "4" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2457 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 309} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "3" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "2" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 327} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2613 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "1" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2015 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2003 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2007 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1963 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 245} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "4" 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: "3" 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: "2" 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: "5" 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: 4.00, per 1000 atoms: 0.22 Number of scatterers: 18419 At special positions: 0 Unit cell: (108.468, 127.512, 133.308, 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 83 16.00 P 11 15.00 Mg 3 11.99 O 3578 8.00 N 3112 7.00 C 11632 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 635.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4490 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 14 sheets defined 53.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.599A pdb=" N ILE 4 23 " --> pdb=" O LEU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 40 Processing helix chain '4' and resid 55 through 68 Processing helix chain '4' and resid 70 through 74 Processing helix chain '4' and resid 85 through 99 removed outlier: 4.072A pdb=" N ILE 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 119 Processing helix chain '4' and resid 120 through 134 removed outlier: 3.781A pdb=" N ARG 4 128 " --> pdb=" O GLN 4 124 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG 4 129 " --> pdb=" O GLN 4 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 4 130 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR 4 134 " --> pdb=" O THR 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 150 Processing helix chain '4' and resid 151 through 157 removed outlier: 3.677A pdb=" N ARG 4 157 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 183 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 201 through 217 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 231 through 241 removed outlier: 3.754A pdb=" N ILE 4 235 " --> pdb=" O PRO 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 255 Processing helix chain '4' and resid 262 through 276 Processing helix chain '4' and resid 281 through 301 Processing helix chain '4' and resid 305 through 321 removed outlier: 3.725A pdb=" N LEU 4 309 " --> pdb=" O THR 4 305 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 13 Processing helix chain '3' and resid 14 through 19 Processing helix chain '3' and resid 23 through 27 removed outlier: 3.734A pdb=" N VAL 3 27 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 44 removed outlier: 3.518A pdb=" N THR 3 36 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 72 Processing helix chain '3' and resid 74 through 78 removed outlier: 3.513A pdb=" N MET 3 78 " --> pdb=" O ASN 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 89 through 103 removed outlier: 4.013A pdb=" N LYS 3 98 " --> pdb=" O ARG 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 122 removed outlier: 3.549A pdb=" N ALA 3 121 " --> pdb=" O GLU 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 137 removed outlier: 4.380A pdb=" N ARG 3 132 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL 3 133 " --> pdb=" O ALA 3 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 160 removed outlier: 3.550A pdb=" N ARG 3 160 " --> pdb=" O ALA 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 185 Processing helix chain '3' and resid 190 through 200 Processing helix chain '3' and resid 204 through 219 Processing helix chain '3' and resid 228 through 237 Processing helix chain '3' and resid 240 through 253 Processing helix chain '3' and resid 255 through 270 removed outlier: 3.801A pdb=" N LYS 3 270 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 286 Processing helix chain '3' and resid 293 through 311 Processing helix chain '3' and resid 315 through 332 Processing helix chain '2' and resid 15 through 24 Processing helix chain '2' and resid 26 through 31 Processing helix chain '2' and resid 42 through 55 removed outlier: 3.620A pdb=" N VAL 2 46 " --> pdb=" O GLN 2 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 48 " --> pdb=" O HIS 2 44 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 88 Proline residue: 2 85 - end of helix Processing helix chain '2' and resid 102 through 116 removed outlier: 3.894A pdb=" N VAL 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 2 111 " --> pdb=" O ARG 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 129 removed outlier: 3.634A pdb=" N LEU 2 126 " --> pdb=" O SER 2 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN 2 128 " --> pdb=" O HIS 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 145 removed outlier: 3.634A pdb=" N SER 2 144 " --> pdb=" O GLU 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 160 removed outlier: 3.557A pdb=" N LEU 2 153 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR 2 156 " --> pdb=" O ALA 2 152 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR 2 160 " --> pdb=" O THR 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 176 Processing helix chain '2' and resid 177 through 184 Processing helix chain '2' and resid 193 through 208 removed outlier: 5.160A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG 2 200 " --> pdb=" O ASN 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 225 Processing helix chain '2' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU 2 245 " --> pdb=" O GLY 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 260 removed outlier: 3.580A pdb=" N LEU 2 259 " --> pdb=" O GLN 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 277 Processing helix chain '2' and resid 279 through 291 Processing helix chain '2' and resid 296 through 311 Processing helix chain '2' and resid 315 through 334 removed outlier: 3.504A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 338 through 352 Processing helix chain '5' and resid 19 through 32 removed outlier: 4.417A pdb=" N GLN 5 32 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 61 Processing helix chain '5' and resid 62 through 66 removed outlier: 3.516A pdb=" N VAL 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 5 66 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 62 through 66' Processing helix chain '5' and resid 97 through 101 removed outlier: 3.964A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 117 removed outlier: 3.692A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 146 Processing helix chain '5' and resid 147 through 161 removed outlier: 4.059A pdb=" N ARG 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 5 157 " --> pdb=" O ALA 5 153 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR 5 161 " --> pdb=" O THR 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 209 Processing helix chain '5' and resid 216 through 227 removed outlier: 4.021A pdb=" N LYS 5 220 " --> pdb=" O LYS 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 229 through 244 removed outlier: 3.529A pdb=" N ASN 5 243 " --> pdb=" O SER 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 257 through 273 Processing helix chain '5' and resid 275 through 291 removed outlier: 3.655A pdb=" N GLU 5 281 " --> pdb=" O ASN 5 277 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 335 Processing helix chain '5' and resid 337 through 353 removed outlier: 3.736A pdb=" N HIS 5 341 " --> pdb=" O LYS 5 337 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY 5 344 " --> pdb=" O PHE 5 340 " (cutoff:3.500A) Processing helix chain '1' and resid 388 through 395 Processing helix chain '1' and resid 398 through 407 Processing helix chain '1' and resid 414 through 430 removed outlier: 3.638A pdb=" N GLY 1 430 " --> pdb=" O VAL 1 426 " (cutoff:3.500A) Processing helix chain '1' and resid 431 through 443 Processing helix chain '1' and resid 453 through 476 removed outlier: 4.087A pdb=" N ALA 1 457 " --> pdb=" O ILE 1 453 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP 1 461 " --> pdb=" O ALA 1 457 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 1 475 " --> pdb=" O GLN 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 479 No H-bonds generated for 'chain '1' and resid 477 through 479' Processing helix chain '1' and resid 480 through 485 removed outlier: 3.859A pdb=" N SER 1 484 " --> pdb=" O LEU 1 480 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 1 485 " --> pdb=" O LEU 1 481 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 485' Processing helix chain '1' and resid 485 through 496 removed outlier: 3.873A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE 1 491 " --> pdb=" O VAL 1 487 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 1 492 " --> pdb=" O PRO 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 534 removed outlier: 3.656A pdb=" N GLU 1 512 " --> pdb=" O ASN 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 542 removed outlier: 3.766A pdb=" N PHE 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 550 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.558A pdb=" N TYR 1 554 " --> pdb=" O GLU 1 550 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 566 Processing helix chain '1' and resid 568 through 586 Processing helix chain '1' and resid 610 through 615 Processing helix chain '1' and resid 617 through 643 removed outlier: 3.675A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.310A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.110A pdb=" N GLN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.107A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 141 through 153 removed outlier: 4.106A pdb=" N GLN C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain '4' and resid 75 through 78 removed outlier: 6.286A pdb=" N LYS 4 109 " --> pdb=" O ARG 4 139 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA 4 141 " --> pdb=" O LYS 4 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE 4 46 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '4' and resid 185 through 186 removed outlier: 7.490A pdb=" N LYS 4 185 " --> pdb=" O VAL 4 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '3' and resid 79 through 82 removed outlier: 6.604A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA 3 147 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE 3 51 " --> pdb=" O ALA 3 147 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 92 through 95 removed outlier: 6.221A pdb=" N LEU 2 62 " --> pdb=" O PHE 2 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 69 through 76 removed outlier: 6.875A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN 5 141 " --> pdb=" O LEU 5 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE 5 96 " --> pdb=" O ASN 5 141 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS 5 136 " --> pdb=" O ARG 5 166 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL 5 138 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL 5 170 " --> pdb=" O VAL 5 138 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE 5 140 " --> pdb=" O VAL 5 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU 5 40 " --> pdb=" O ILE 5 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 212 through 213 removed outlier: 5.834A pdb=" N GLN 5 212 " --> pdb=" O LEU 5 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '1' and resid 589 through 592 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU A 59 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU A 25 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 40 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 240 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG A 224 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.289A pdb=" N SER A 157 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP A 172 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 177 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 181 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 111 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 59 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 172 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 157 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU B 25 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 40 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP B 240 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B 224 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 177 through 182 removed outlier: 4.663A pdb=" N ASP B 172 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER B 157 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU C 25 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 40 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 244 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP C 240 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG C 224 " --> pdb=" O ASP C 240 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 3150 1.26 - 1.43: 4482 1.43 - 1.61: 10947 1.61 - 1.78: 11 1.78 - 1.95: 119 Bond restraints: 18709 Sorted by residual: bond pdb=" C GLU B 258 " pdb=" OXT GLU B 258 " ideal model delta sigma weight residual 1.231 1.091 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C GLU B 258 " pdb=" O GLU B 258 " ideal model delta sigma weight residual 1.231 1.371 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C GLU A 258 " pdb=" OXT GLU A 258 " ideal model delta sigma weight residual 1.231 1.091 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C GLU A 258 " pdb=" O GLU A 258 " ideal model delta sigma weight residual 1.231 1.369 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C4 ADP 5 401 " pdb=" C5 ADP 5 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 18704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 24492 3.06 - 6.13: 756 6.13 - 9.19: 67 9.19 - 12.26: 10 12.26 - 15.32: 7 Bond angle restraints: 25332 Sorted by residual: angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 110.41 122.91 -12.50 1.18e+00 7.18e-01 1.12e+02 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" C GLU B 257 " ideal model delta sigma weight residual 110.41 122.90 -12.49 1.18e+00 7.18e-01 1.12e+02 angle pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" C ASP B 97 " ideal model delta sigma weight residual 113.72 104.47 9.25 1.30e+00 5.92e-01 5.06e+01 angle pdb=" N ASP C 97 " pdb=" CA ASP C 97 " pdb=" C ASP C 97 " ideal model delta sigma weight residual 113.72 104.62 9.10 1.30e+00 5.92e-01 4.90e+01 angle pdb=" N ASP A 97 " pdb=" CA ASP A 97 " pdb=" C ASP A 97 " ideal model delta sigma weight residual 113.72 104.67 9.05 1.30e+00 5.92e-01 4.85e+01 ... (remaining 25327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 10960 25.42 - 50.85: 448 50.85 - 76.27: 82 76.27 - 101.69: 22 101.69 - 127.11: 3 Dihedral angle restraints: 11515 sinusoidal: 4629 harmonic: 6886 Sorted by residual: dihedral pdb=" O2A ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PA ADP 5 401 " pdb=" PB ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.69 -120.69 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" O1B ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PB ADP 5 401 " pdb=" PA ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 48.55 -108.55 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CA GLU B 257 " pdb=" CB GLU B 257 " ideal model delta harmonic sigma weight residual 122.80 134.76 -11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 11512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2594 0.119 - 0.238: 301 0.238 - 0.356: 61 0.356 - 0.475: 12 0.475 - 0.594: 5 Chirality restraints: 2973 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" CA CYS C 22 " pdb=" N CYS C 22 " pdb=" C CYS C 22 " pdb=" CB CYS C 22 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 2970 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 258 " 0.037 2.00e-02 2.50e+03 8.20e-02 6.72e+01 pdb=" C GLU A 258 " -0.141 2.00e-02 2.50e+03 pdb=" O GLU A 258 " 0.042 2.00e-02 2.50e+03 pdb=" OXT GLU A 258 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 258 " 0.037 2.00e-02 2.50e+03 8.14e-02 6.63e+01 pdb=" C GLU B 258 " -0.140 2.00e-02 2.50e+03 pdb=" O GLU B 258 " 0.042 2.00e-02 2.50e+03 pdb=" OXT GLU B 258 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 563 " -0.087 2.00e-02 2.50e+03 5.81e-02 5.92e+01 pdb=" CG PHE 1 563 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 563 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 563 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 563 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE 1 563 " -0.081 2.00e-02 2.50e+03 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 32 2.40 - 3.02: 10571 3.02 - 3.65: 26983 3.65 - 4.27: 41786 4.27 - 4.90: 69871 Nonbonded interactions: 149243 Sorted by model distance: nonbonded pdb=" O ASP A 109 " pdb=" O ILE B 181 " model vdw 1.772 3.040 nonbonded pdb=" OD2 ASP 4 265 " pdb=" OH TYR 3 52 " model vdw 2.049 3.040 nonbonded pdb=" O3G AGS 3 401 " pdb="MG MG 3 402 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR 4 56 " pdb="MG MG 4 402 " model vdw 2.122 2.170 nonbonded pdb=" OD1 ASP 3 229 " pdb=" OD1 ASP 3 230 " model vdw 2.123 3.040 ... (remaining 149238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 83 or (resid 84 and (n \ ame N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 96 or ( \ resid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 th \ rough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 or (resid 119 and (name N or name CA or name C or name O or name C \ B )) or resid 120 through 125 or (resid 126 and (name N or name CA or name C or \ name O or name CB )) or resid 127 through 173 or (resid 174 and (name N or name \ CA or name C or name O or name CB )) or resid 175 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB )) or resid 237 through 254)) selection = (chain 'B' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 43 or (resid 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 173 or (resid 174 and (name N o \ r name CA or name C or name O or name CB )) or resid 175 through 235 or (resid 2 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 237 through \ 254)) selection = (chain 'C' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 or (resid 72 and (name N or name CA or na \ me C or name O or name CB )) or resid 73 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 109 or (resid 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 through 11 \ 8 or (resid 119 and (name N or name CA or name C or name O or name CB )) or resi \ d 120 through 252 or (resid 253 and (name N or name CA or name C or name O or na \ me CB )) or resid 254)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.480 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.009 0.140 18709 Z= 0.506 Angle : 1.199 15.323 25332 Z= 0.775 Chirality : 0.088 0.594 2973 Planarity : 0.010 0.184 3239 Dihedral : 14.614 127.113 7025 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.26 % Favored : 95.88 % Rotamer: Outliers : 0.54 % Allowed : 6.76 % Favored : 92.69 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.16), residues: 2331 helix: -0.49 (0.14), residues: 1103 sheet: 0.11 (0.22), residues: 505 loop : -1.80 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG C 224 TYR 0.078 0.006 TYR C 133 PHE 0.087 0.009 PHE 1 563 TRP 0.038 0.003 TRP 1 399 HIS 0.007 0.001 HIS 1 466 Details of bonding type rmsd covalent geometry : bond 0.00864 (18709) covalent geometry : angle 1.19868 (25332) hydrogen bonds : bond 0.15459 ( 1065) hydrogen bonds : angle 6.30165 ( 3015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 489 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7265 (pp) REVERT: 2 20 GLN cc_start: 0.7888 (mm-40) cc_final: 0.6958 (tp40) REVERT: 2 118 VAL cc_start: 0.7166 (m) cc_final: 0.6563 (m) REVERT: 2 140 ASP cc_start: 0.8211 (t0) cc_final: 0.8005 (t0) REVERT: 2 169 ILE cc_start: 0.7648 (mt) cc_final: 0.7274 (mt) REVERT: 5 159 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7242 (mt-10) REVERT: A 150 ASP cc_start: 0.7200 (m-30) cc_final: 0.6990 (m-30) REVERT: C 119 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7326 (mtt) REVERT: C 198 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8334 (mt-10) outliers start: 11 outliers final: 2 residues processed: 494 average time/residue: 0.1650 time to fit residues: 119.6881 Evaluate side-chains 262 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 257 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 18 GLN 4 60 HIS 4 92 GLN 4 177 GLN 4 220 ASN 4 244 ASN 4 320 ASN 3 180 ASN 3 317 GLN 2 60 HIS 2 96 ASN 2 150 GLN 2 303 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 80 ASN 5 86 ASN 5 244 ASN 1 425 GLN A 64 HIS A 159 ASN A 247 GLN B 159 ASN C 24 GLN C 64 HIS C 83 ASN C 94 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.133243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.113809 restraints weight = 45413.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.114342 restraints weight = 32852.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115068 restraints weight = 23293.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115408 restraints weight = 19970.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115608 restraints weight = 17630.116| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18709 Z= 0.178 Angle : 0.632 9.293 25332 Z= 0.327 Chirality : 0.043 0.194 2973 Planarity : 0.005 0.090 3239 Dihedral : 8.004 119.180 2586 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.73 % Allowed : 13.03 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.17), residues: 2331 helix: 0.80 (0.15), residues: 1109 sheet: 0.47 (0.22), residues: 506 loop : -1.34 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 1 434 TYR 0.022 0.002 TYR 1 483 PHE 0.026 0.002 PHE 5 345 TRP 0.014 0.002 TRP 1 399 HIS 0.008 0.001 HIS 5 38 Details of bonding type rmsd covalent geometry : bond 0.00396 (18709) covalent geometry : angle 0.63183 (25332) hydrogen bonds : bond 0.04214 ( 1065) hydrogen bonds : angle 4.98511 ( 3015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7120 (pp) REVERT: 4 50 MET cc_start: 0.7455 (mpp) cc_final: 0.7104 (mtt) REVERT: 4 202 MET cc_start: 0.6040 (tpp) cc_final: 0.5774 (tpp) REVERT: 3 21 PRO cc_start: 0.7906 (Cg_exo) cc_final: 0.7690 (Cg_endo) REVERT: 2 140 ASP cc_start: 0.8524 (t0) cc_final: 0.7956 (m-30) REVERT: 5 101 MET cc_start: 0.7761 (ptp) cc_final: 0.7504 (ptp) REVERT: 5 184 ARG cc_start: 0.7056 (mtt90) cc_final: 0.6736 (mtt90) REVERT: 1 413 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7603 (mtp180) REVERT: 1 417 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6514 (tm-30) REVERT: 1 621 ILE cc_start: 0.8104 (mt) cc_final: 0.7886 (tt) REVERT: 1 631 ASN cc_start: 0.5862 (m110) cc_final: 0.5658 (m110) REVERT: A 161 MET cc_start: 0.8311 (ttt) cc_final: 0.8061 (ttp) REVERT: B 156 ASP cc_start: 0.7470 (t0) cc_final: 0.7243 (t0) REVERT: B 199 MET cc_start: 0.7012 (ttm) cc_final: 0.6686 (ttm) REVERT: B 211 TYR cc_start: 0.7709 (m-80) cc_final: 0.7341 (m-80) REVERT: C 25 LEU cc_start: 0.8336 (mt) cc_final: 0.7583 (mt) REVERT: C 46 LEU cc_start: 0.7598 (mp) cc_final: 0.6951 (tt) outliers start: 35 outliers final: 20 residues processed: 293 average time/residue: 0.1286 time to fit residues: 58.2351 Evaluate side-chains 240 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 113 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 5 residue 134 ARG Chi-restraints excluded: chain 5 residue 215 THR Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 570 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 317 HIS 3 148 ASN 2 25 GLN 2 150 GLN ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 244 ASN 1 534 GLN 1 617 ASN A 29 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.129133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.109636 restraints weight = 45627.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108209 restraints weight = 37658.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109481 restraints weight = 26692.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.109738 restraints weight = 21955.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109877 restraints weight = 20579.438| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18709 Z= 0.167 Angle : 0.579 8.537 25332 Z= 0.299 Chirality : 0.042 0.164 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.615 118.144 2578 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.12 % Allowed : 14.36 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2331 helix: 1.20 (0.16), residues: 1090 sheet: 0.40 (0.22), residues: 504 loop : -1.22 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 1 434 TYR 0.015 0.001 TYR A 211 PHE 0.026 0.002 PHE 5 345 TRP 0.007 0.001 TRP 4 11 HIS 0.006 0.001 HIS 5 38 Details of bonding type rmsd covalent geometry : bond 0.00380 (18709) covalent geometry : angle 0.57937 (25332) hydrogen bonds : bond 0.03755 ( 1065) hydrogen bonds : angle 4.75539 ( 3015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7435 (pp) REVERT: 4 50 MET cc_start: 0.7461 (mpp) cc_final: 0.7061 (mtt) REVERT: 4 119 MET cc_start: 0.5698 (OUTLIER) cc_final: 0.5380 (mtm) REVERT: 4 185 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7997 (mmtm) REVERT: 4 186 TYR cc_start: 0.9015 (p90) cc_final: 0.8667 (p90) REVERT: 4 202 MET cc_start: 0.6149 (tpp) cc_final: 0.5791 (tpp) REVERT: 4 271 PHE cc_start: 0.7768 (t80) cc_final: 0.7138 (t80) REVERT: 2 140 ASP cc_start: 0.8536 (t0) cc_final: 0.7958 (m-30) REVERT: 5 299 ILE cc_start: 0.6630 (OUTLIER) cc_final: 0.6262 (mt) REVERT: 5 342 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7976 (mm) REVERT: 1 413 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7553 (mtp180) REVERT: 1 417 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6635 (tm-30) REVERT: 1 483 TYR cc_start: 0.7825 (m-80) cc_final: 0.7582 (m-80) REVERT: 1 631 ASN cc_start: 0.5772 (m110) cc_final: 0.5561 (m110) REVERT: A 117 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7586 (tmtp) REVERT: C 51 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7629 (tt0) outliers start: 43 outliers final: 26 residues processed: 258 average time/residue: 0.1441 time to fit residues: 56.2236 Evaluate side-chains 237 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 82 ASP Chi-restraints excluded: chain 4 residue 119 MET Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 113 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 85 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 145 ASN 2 124 HIS 2 321 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 508 ASN ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.125299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.103928 restraints weight = 45902.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.104010 restraints weight = 31158.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104894 restraints weight = 24307.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105096 restraints weight = 19828.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105221 restraints weight = 18210.936| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18709 Z= 0.179 Angle : 0.583 7.968 25332 Z= 0.299 Chirality : 0.042 0.198 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.586 118.603 2578 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.37 % Allowed : 15.70 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.17), residues: 2331 helix: 1.25 (0.16), residues: 1089 sheet: 0.38 (0.22), residues: 499 loop : -1.16 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 184 TYR 0.016 0.002 TYR B 211 PHE 0.025 0.002 PHE 5 345 TRP 0.006 0.001 TRP 4 11 HIS 0.011 0.001 HIS 2 340 Details of bonding type rmsd covalent geometry : bond 0.00414 (18709) covalent geometry : angle 0.58286 (25332) hydrogen bonds : bond 0.03650 ( 1065) hydrogen bonds : angle 4.74516 ( 3015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.677 Fit side-chains REVERT: 4 7 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7408 (pp) REVERT: 4 185 LYS cc_start: 0.8286 (mmtm) cc_final: 0.8016 (mmtm) REVERT: 4 186 TYR cc_start: 0.9034 (p90) cc_final: 0.8617 (p90) REVERT: 4 271 PHE cc_start: 0.7963 (t80) cc_final: 0.7382 (t80) REVERT: 5 342 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7876 (mm) REVERT: 1 413 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.7584 (mtp180) REVERT: 1 417 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6836 (tm-30) REVERT: 1 514 ARG cc_start: 0.5752 (ttt180) cc_final: 0.3344 (mtm110) REVERT: A 175 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7625 (mt) REVERT: B 49 SER cc_start: 0.8549 (m) cc_final: 0.8243 (t) REVERT: B 256 ASP cc_start: 0.7579 (m-30) cc_final: 0.7121 (p0) REVERT: C 7 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7448 (tp30) outliers start: 48 outliers final: 27 residues processed: 253 average time/residue: 0.1423 time to fit residues: 54.4031 Evaluate side-chains 229 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 296 SER Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 215 THR Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 162 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 113 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 148 ASN 2 150 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 418 GLN ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.126656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.105643 restraints weight = 45460.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.105894 restraints weight = 29413.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106757 restraints weight = 22553.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106985 restraints weight = 18535.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107068 restraints weight = 16663.861| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18709 Z= 0.114 Angle : 0.524 7.356 25332 Z= 0.269 Chirality : 0.040 0.193 2973 Planarity : 0.004 0.056 3239 Dihedral : 7.326 116.688 2574 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.83 % Allowed : 16.44 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2331 helix: 1.47 (0.16), residues: 1080 sheet: 0.30 (0.22), residues: 511 loop : -0.95 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 184 TYR 0.011 0.001 TYR 2 286 PHE 0.026 0.001 PHE 5 345 TRP 0.006 0.001 TRP 1 399 HIS 0.013 0.001 HIS 2 340 Details of bonding type rmsd covalent geometry : bond 0.00255 (18709) covalent geometry : angle 0.52387 (25332) hydrogen bonds : bond 0.03266 ( 1065) hydrogen bonds : angle 4.56441 ( 3015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7432 (pp) REVERT: 4 185 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7835 (mmtm) REVERT: 4 186 TYR cc_start: 0.9031 (p90) cc_final: 0.8565 (p90) REVERT: 4 271 PHE cc_start: 0.7936 (t80) cc_final: 0.7427 (t80) REVERT: 5 299 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6684 (mt) REVERT: 1 413 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7614 (mtp180) REVERT: 1 417 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6692 (tm-30) REVERT: B 49 SER cc_start: 0.8516 (m) cc_final: 0.8155 (t) REVERT: B 211 TYR cc_start: 0.7781 (m-80) cc_final: 0.7159 (m-80) REVERT: C 7 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: C 51 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7584 (tt0) outliers start: 37 outliers final: 23 residues processed: 241 average time/residue: 0.1477 time to fit residues: 54.4517 Evaluate side-chains 222 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 158 LEU Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 150 GLN Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 155 GLN 3 213 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 38 HIS 5 208 ASN 5 341 HIS 1 418 GLN ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.122318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.100771 restraints weight = 46009.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.100278 restraints weight = 30789.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101127 restraints weight = 26660.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101407 restraints weight = 21110.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.101538 restraints weight = 19648.616| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18709 Z= 0.244 Angle : 0.639 7.806 25332 Z= 0.326 Chirality : 0.043 0.163 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.522 117.596 2574 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.71 % Allowed : 16.29 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2331 helix: 1.18 (0.16), residues: 1079 sheet: 0.15 (0.22), residues: 514 loop : -1.12 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 88 TYR 0.018 0.002 TYR 3 288 PHE 0.023 0.002 PHE 5 345 TRP 0.009 0.002 TRP 5 259 HIS 0.006 0.001 HIS 2 340 Details of bonding type rmsd covalent geometry : bond 0.00570 (18709) covalent geometry : angle 0.63865 (25332) hydrogen bonds : bond 0.03910 ( 1065) hydrogen bonds : angle 4.87741 ( 3015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.785 Fit side-chains REVERT: 4 7 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7605 (pp) REVERT: 4 119 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.5651 (mtm) REVERT: 4 185 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7913 (mmtm) REVERT: 4 202 MET cc_start: 0.5673 (tpp) cc_final: 0.5252 (tpp) REVERT: 4 271 PHE cc_start: 0.7949 (t80) cc_final: 0.7449 (t80) REVERT: 3 131 ARG cc_start: 0.8097 (ptt180) cc_final: 0.7761 (ptt180) REVERT: 5 299 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6884 (mt) REVERT: 1 413 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7620 (mtp180) REVERT: 1 417 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6828 (tm-30) REVERT: 1 514 ARG cc_start: 0.5745 (ttt180) cc_final: 0.3351 (mtm110) REVERT: A 175 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7827 (mt) REVERT: B 49 SER cc_start: 0.8548 (m) cc_final: 0.8238 (t) REVERT: B 256 ASP cc_start: 0.7602 (m-30) cc_final: 0.7402 (p0) REVERT: C 7 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7461 (tp30) REVERT: C 51 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7708 (tt0) outliers start: 55 outliers final: 37 residues processed: 239 average time/residue: 0.1419 time to fit residues: 51.9802 Evaluate side-chains 234 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 119 MET Chi-restraints excluded: chain 4 residue 290 LYS Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 158 LEU Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 2 residue 329 THR Chi-restraints excluded: chain 5 residue 215 THR Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 300 LEU Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain 1 residue 481 LEU Chi-restraints excluded: chain 1 residue 502 ASP Chi-restraints excluded: chain 1 residue 570 LYS Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 71 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 128 ASN 2 25 GLN 2 171 ASN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 617 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.122292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.100765 restraints weight = 45962.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100304 restraints weight = 30563.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100964 restraints weight = 25749.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101438 restraints weight = 20768.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101463 restraints weight = 19241.710| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 18709 Z= 0.205 Angle : 0.593 6.674 25332 Z= 0.306 Chirality : 0.042 0.165 2973 Planarity : 0.004 0.058 3239 Dihedral : 7.568 117.971 2574 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.47 % Allowed : 17.37 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2331 helix: 1.09 (0.16), residues: 1092 sheet: 0.08 (0.22), residues: 514 loop : -1.16 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 155 TYR 0.015 0.002 TYR 3 288 PHE 0.026 0.002 PHE 5 345 TRP 0.008 0.001 TRP 5 259 HIS 0.005 0.001 HIS 5 93 Details of bonding type rmsd covalent geometry : bond 0.00482 (18709) covalent geometry : angle 0.59341 (25332) hydrogen bonds : bond 0.03738 ( 1065) hydrogen bonds : angle 4.82174 ( 3015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 0.693 Fit side-chains REVERT: 4 7 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7714 (pp) REVERT: 4 185 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7995 (mmtm) REVERT: 4 271 PHE cc_start: 0.7960 (t80) cc_final: 0.7459 (t80) REVERT: 3 131 ARG cc_start: 0.8131 (ptt180) cc_final: 0.7855 (ptt180) REVERT: 3 256 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.6739 (t60) REVERT: 5 299 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6990 (mt) REVERT: 1 413 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7623 (mtp180) REVERT: 1 417 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6582 (tm-30) REVERT: 1 514 ARG cc_start: 0.5678 (ttt180) cc_final: 0.3277 (mtm110) REVERT: B 7 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: B 49 SER cc_start: 0.8474 (m) cc_final: 0.8170 (t) REVERT: C 51 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: C 199 MET cc_start: 0.8183 (ttt) cc_final: 0.7033 (ttt) outliers start: 50 outliers final: 35 residues processed: 234 average time/residue: 0.1316 time to fit residues: 47.2252 Evaluate side-chains 230 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 164 THR Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 392 ASN Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain 1 residue 502 ASP Chi-restraints excluded: chain 1 residue 570 LYS Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 225 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 98 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 182 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.122622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.101166 restraints weight = 45585.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.100700 restraints weight = 30596.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101595 restraints weight = 25504.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101785 restraints weight = 20558.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101968 restraints weight = 18563.649| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18709 Z= 0.175 Angle : 0.576 6.985 25332 Z= 0.296 Chirality : 0.041 0.163 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.559 118.984 2574 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.67 % Allowed : 17.23 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.18), residues: 2331 helix: 1.18 (0.16), residues: 1092 sheet: 0.04 (0.23), residues: 512 loop : -1.11 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 155 TYR 0.021 0.001 TYR 2 134 PHE 0.023 0.002 PHE 5 345 TRP 0.007 0.001 TRP 5 259 HIS 0.004 0.001 HIS 1 626 Details of bonding type rmsd covalent geometry : bond 0.00410 (18709) covalent geometry : angle 0.57610 (25332) hydrogen bonds : bond 0.03621 ( 1065) hydrogen bonds : angle 4.76261 ( 3015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 194 time to evaluate : 0.707 Fit side-chains REVERT: 4 7 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7759 (pp) REVERT: 4 185 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7944 (mmtm) REVERT: 4 271 PHE cc_start: 0.7955 (t80) cc_final: 0.7487 (t80) REVERT: 3 131 ARG cc_start: 0.8100 (ptt180) cc_final: 0.7822 (ptt180) REVERT: 3 256 TRP cc_start: 0.8662 (OUTLIER) cc_final: 0.6776 (t60) REVERT: 5 299 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6942 (mt) REVERT: 1 576 MET cc_start: 0.6394 (mmm) cc_final: 0.5671 (mmt) REVERT: A 175 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7883 (mt) REVERT: B 7 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: B 49 SER cc_start: 0.8496 (m) cc_final: 0.8154 (t) REVERT: C 51 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: C 113 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6175 (tm-30) REVERT: C 199 MET cc_start: 0.8208 (ttt) cc_final: 0.7120 (ttt) REVERT: C 211 TYR cc_start: 0.7256 (m-80) cc_final: 0.7007 (m-80) outliers start: 54 outliers final: 40 residues processed: 234 average time/residue: 0.1221 time to fit residues: 43.8369 Evaluate side-chains 234 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 164 THR Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 296 SER Chi-restraints excluded: chain 2 residue 353 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 300 LEU Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 392 ASN Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain 1 residue 481 LEU Chi-restraints excluded: chain 1 residue 570 LYS Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 225 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 219 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 197 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 170 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 128 ASN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS B 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.102857 restraints weight = 45396.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102515 restraints weight = 30069.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103373 restraints weight = 25580.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103750 restraints weight = 20192.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.103694 restraints weight = 18670.863| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18709 Z= 0.122 Angle : 0.540 7.022 25332 Z= 0.277 Chirality : 0.040 0.162 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.399 117.053 2574 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.02 % Allowed : 18.16 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.18), residues: 2331 helix: 1.32 (0.16), residues: 1095 sheet: 0.12 (0.23), residues: 512 loop : -1.00 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG 2 155 TYR 0.019 0.001 TYR 2 134 PHE 0.025 0.001 PHE 5 345 TRP 0.005 0.001 TRP 5 259 HIS 0.004 0.001 HIS 1 626 Details of bonding type rmsd covalent geometry : bond 0.00280 (18709) covalent geometry : angle 0.53984 (25332) hydrogen bonds : bond 0.03342 ( 1065) hydrogen bonds : angle 4.61525 ( 3015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.444 Fit side-chains REVERT: 4 7 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7731 (pp) REVERT: 4 67 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.6017 (mt) REVERT: 4 185 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7981 (mmtm) REVERT: 4 186 TYR cc_start: 0.8956 (p90) cc_final: 0.8684 (p90) REVERT: 4 271 PHE cc_start: 0.7950 (t80) cc_final: 0.7495 (t80) REVERT: 3 131 ARG cc_start: 0.8090 (ptt180) cc_final: 0.7819 (ptt180) REVERT: 3 256 TRP cc_start: 0.8637 (OUTLIER) cc_final: 0.6730 (t60) REVERT: 5 299 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6884 (mt) REVERT: 1 413 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7596 (mtp180) REVERT: 1 576 MET cc_start: 0.6297 (mmm) cc_final: 0.5554 (mmt) REVERT: B 7 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: B 49 SER cc_start: 0.8486 (m) cc_final: 0.8130 (t) REVERT: C 113 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: C 211 TYR cc_start: 0.7147 (m-80) cc_final: 0.6904 (m-80) outliers start: 41 outliers final: 30 residues processed: 231 average time/residue: 0.1274 time to fit residues: 45.3036 Evaluate side-chains 228 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 205 MET Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 43 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 2 residue 353 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 8 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 25 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN B 94 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.121647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100989 restraints weight = 45632.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100267 restraints weight = 32854.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.101087 restraints weight = 27609.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102442 restraints weight = 20878.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.102342 restraints weight = 18006.310| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18709 Z= 0.209 Angle : 0.619 7.928 25332 Z= 0.316 Chirality : 0.043 0.160 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.547 118.916 2574 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.07 % Allowed : 18.36 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.18), residues: 2331 helix: 1.16 (0.16), residues: 1087 sheet: 0.03 (0.23), residues: 512 loop : -1.10 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 2 155 TYR 0.027 0.002 TYR 2 134 PHE 0.027 0.002 PHE 5 345 TRP 0.008 0.001 TRP 5 259 HIS 0.017 0.001 HIS 2 340 Details of bonding type rmsd covalent geometry : bond 0.00492 (18709) covalent geometry : angle 0.61875 (25332) hydrogen bonds : bond 0.03782 ( 1065) hydrogen bonds : angle 4.83111 ( 3015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.617 Fit side-chains REVERT: 4 7 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7829 (pp) REVERT: 4 67 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.6087 (mt) REVERT: 4 185 LYS cc_start: 0.8148 (mmtm) cc_final: 0.7896 (mmtm) REVERT: 4 186 TYR cc_start: 0.8947 (p90) cc_final: 0.8655 (p90) REVERT: 4 271 PHE cc_start: 0.7944 (t80) cc_final: 0.7481 (t80) REVERT: 3 131 ARG cc_start: 0.8104 (ptt180) cc_final: 0.7815 (ptm160) REVERT: 3 256 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.6809 (t60) REVERT: 5 299 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6939 (mt) REVERT: 1 413 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7508 (mtp180) REVERT: A 175 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7840 (mt) REVERT: B 7 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: B 49 SER cc_start: 0.8494 (m) cc_final: 0.8169 (t) REVERT: C 113 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6201 (tm-30) REVERT: C 199 MET cc_start: 0.7935 (tpp) cc_final: 0.7396 (ttt) REVERT: C 211 TYR cc_start: 0.7243 (m-80) cc_final: 0.6993 (m-80) outliers start: 42 outliers final: 33 residues processed: 224 average time/residue: 0.1157 time to fit residues: 40.0338 Evaluate side-chains 227 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 62 THR Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 151 HIS Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 43 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 104 SER Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 300 LEU Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 431 ASN Chi-restraints excluded: chain 1 residue 481 LEU Chi-restraints excluded: chain 1 residue 502 ASP Chi-restraints excluded: chain 1 residue 570 LYS Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 3 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 124 GLN 2 25 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100928 restraints weight = 45742.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101359 restraints weight = 33114.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.101806 restraints weight = 28051.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102036 restraints weight = 19619.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.102262 restraints weight = 18886.734| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18709 Z= 0.191 Angle : 0.603 8.751 25332 Z= 0.308 Chirality : 0.042 0.165 2973 Planarity : 0.004 0.057 3239 Dihedral : 7.536 119.638 2574 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.37 % Allowed : 18.02 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.18), residues: 2331 helix: 1.11 (0.16), residues: 1086 sheet: 0.00 (0.23), residues: 512 loop : -1.05 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 155 TYR 0.019 0.001 TYR 2 134 PHE 0.028 0.002 PHE 5 345 TRP 0.008 0.001 TRP 5 259 HIS 0.009 0.001 HIS 2 340 Details of bonding type rmsd covalent geometry : bond 0.00450 (18709) covalent geometry : angle 0.60257 (25332) hydrogen bonds : bond 0.03703 ( 1065) hydrogen bonds : angle 4.82402 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2708.64 seconds wall clock time: 47 minutes 53.94 seconds (2873.94 seconds total)