Starting phenix.real_space_refine on Mon May 19 17:14:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twb_41665/05_2025/8twb_41665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twb_41665/05_2025/8twb_41665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twb_41665/05_2025/8twb_41665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twb_41665/05_2025/8twb_41665.map" model { file = "/net/cci-nas-00/data/ceres_data/8twb_41665/05_2025/8twb_41665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twb_41665/05_2025/8twb_41665.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.067 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 46 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 11991 2.51 5 N 3248 2.21 5 O 3795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19167 Number of models: 1 Model: "" Number of chains: 14 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: {'GLU:plan': 3, 'HIS:plan': 1} 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: 2677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2677 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 327} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2639 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 323} 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: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS: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: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2} 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: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2010 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: "T" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 11.62, per 1000 atoms: 0.61 Number of scatterers: 19167 At special positions: 0 Unit cell: (125.028, 123.372, 125.856, 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 84 16.00 P 46 15.00 Mg 3 11.99 O 3795 8.00 N 3248 7.00 C 11991 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: 5.11 Conformation dependent library (CDL) restraints added in 2.5 seconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 14 sheets defined 54.0% alpha, 16.0% beta 13 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 6.44 Creating SS restraints... Processing helix chain '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.598A 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: 4.315A 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: 3.878A 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: 3.514A 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: 3.548A 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: 3.551A 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: 3.619A 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: 3.539A 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: 3.893A 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: 3.850A 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: 3.760A 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: 4.169A 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: 5.663A 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: 3.579A 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: 4.416A 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: 3.517A 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: 3.963A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 120 removed outlier: 3.692A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU 5 120 " --> pdb=" O VAL 5 116 " (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: 3.866A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.579A 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: 4.022A pdb=" N LYS 5 220 " --> pdb=" O LYS 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 229 through 244 removed outlier: 3.530A 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: 3.654A 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: 3.737A pdb=" N HIS 5 341 " --> pdb=" O LYS 5 337 " (cutoff:3.500A) removed outlier: 3.837A 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: 3.636A 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: 4.088A pdb=" N ALA 1 457 " --> pdb=" O ILE 1 453 " (cutoff:3.500A) removed outlier: 3.579A 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: 3.860A 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: 3.872A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.856A 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: 3.676A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.309A 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: 3.656A 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: 4.108A 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: 4.308A pdb=" N PHE C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.655A 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: 6.227A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.246A 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: 7.488A 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: 6.605A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.944A 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: 6.122A 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: 6.220A 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 74 removed outlier: 6.875A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.721A 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: 7.982A 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: 6.490A 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: 4.446A pdb=" N VAL A 40 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.902A 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: 4.662A pdb=" N ASP A 172 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 177 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 181 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 111 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.522A pdb=" N GLU B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.661A 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: 5.538A pdb=" N LEU B 25 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 40 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.698A 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: 7.069A 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: 4.661A pdb=" N ASP B 172 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.290A 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: 5.538A 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: 3.697A 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: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 6.73 Time building geometry restraints manager: 5.90 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: 3191 1.26 - 1.43: 4875 1.43 - 1.61: 11334 1.61 - 1.78: 22 1.78 - 1.95: 121 Bond restraints: 19543 Sorted by residual: bond pdb=" C GLU A 258 " pdb=" OXT GLU A 258 " ideal model delta sigma weight residual 1.231 1.090 0.141 2.00e-02 2.50e+03 4.99e+01 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 1.370 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C GLU A 258 " pdb=" O GLU A 258 " ideal model delta sigma weight residual 1.231 1.368 -0.137 2.00e-02 2.50e+03 4.72e+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 2.99e+01 ... (remaining 19538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 25653 3.08 - 6.15: 834 6.15 - 9.23: 103 9.23 - 12.31: 10 12.31 - 15.39: 7 Bond angle restraints: 26607 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 110.41 122.85 -12.44 1.18e+00 7.18e-01 1.11e+02 angle pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" C ASP B 97 " ideal model delta sigma weight residual 113.72 104.53 9.19 1.30e+00 5.92e-01 5.00e+01 angle pdb=" N ASP C 97 " pdb=" CA ASP C 97 " pdb=" C ASP C 97 " ideal model delta sigma weight residual 113.72 104.63 9.09 1.30e+00 5.92e-01 4.89e+01 angle pdb=" N ASP A 97 " pdb=" CA ASP A 97 " pdb=" C ASP A 97 " ideal model delta sigma weight residual 113.72 104.68 9.04 1.30e+00 5.92e-01 4.84e+01 ... (remaining 26602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.35: 11131 26.35 - 52.71: 629 52.71 - 79.06: 138 79.06 - 105.41: 18 105.41 - 131.77: 3 Dihedral angle restraints: 11919 sinusoidal: 5024 harmonic: 6895 Sorted by residual: 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 300.00 168.23 131.77 1 2.00e+01 2.50e-03 4.00e+01 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 60.76 -120.76 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta harmonic sigma weight residual 122.80 134.85 -12.05 0 2.50e+00 1.60e-01 2.32e+01 ... (remaining 11916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2755 0.124 - 0.249: 285 0.249 - 0.373: 56 0.373 - 0.498: 13 0.498 - 0.622: 7 Chirality restraints: 3116 Sorted by residual: chirality pdb=" P DA T 1 " pdb=" OP1 DA T 1 " pdb=" OP2 DA T 1 " pdb=" O5' DA T 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.69e+00 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 1.91 0.60 2.00e-01 2.50e+01 8.95e+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 8.71e+00 ... (remaining 3113 not shown) Planarity restraints: 3280 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 8.17e-02 6.68e+01 pdb=" C GLU B 258 " 0.141 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 5.82e-02 5.92e+01 pdb=" CG PHE 1 563 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 563 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 563 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 563 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 563 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 1 563 " -0.081 2.00e-02 2.50e+03 ... (remaining 3277 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 229 2.62 - 3.19: 16555 3.19 - 3.76: 29600 3.76 - 4.33: 41973 4.33 - 4.90: 68060 Nonbonded interactions: 156417 Sorted by model distance: nonbonded pdb=" OD2 ASP 4 265 " pdb=" OH TYR 3 52 " model vdw 2.048 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=" O3G AGS 4 401 " pdb="MG MG 4 402 " model vdw 2.124 2.170 nonbonded pdb=" OG1 THR 3 60 " pdb="MG MG 3 402 " model vdw 2.124 2.170 ... (remaining 156412 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 96 or (resid 97 and (name N or name CA or name C or name O or n \ ame CB )) or resid 98 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 n \ ame 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 23 \ 5 or (resid 236 and (name N or name CA or name C or name O or name CB )) or resi \ d 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 48.310 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 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 0.141 19543 Z= 0.509 Angle : 1.232 15.385 26607 Z= 0.792 Chirality : 0.089 0.622 3116 Planarity : 0.009 0.185 3280 Dihedral : 16.558 131.768 7423 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.26 % Favored : 95.89 % Rotamer: Outliers : 0.64 % Allowed : 6.75 % Favored : 92.61 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2334 helix: -0.50 (0.14), residues: 1105 sheet: 0.10 (0.22), residues: 505 loop : -1.81 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP 1 399 HIS 0.008 0.001 HIS 4 296 PHE 0.087 0.010 PHE 1 563 TYR 0.078 0.006 TYR A 133 ARG 0.028 0.002 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.15462 ( 1096) hydrogen bonds : angle 6.28535 ( 3077) covalent geometry : bond 0.00888 (19543) covalent geometry : angle 1.23209 (26607) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 371 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 19 VAL cc_start: 0.8661 (t) cc_final: 0.8417 (p) REVERT: 2 88 MET cc_start: 0.6990 (tpt) cc_final: 0.6769 (tpp) REVERT: 5 101 MET cc_start: 0.8037 (ptt) cc_final: 0.7433 (ptm) REVERT: 5 105 ASP cc_start: 0.6109 (m-30) cc_final: 0.5832 (m-30) REVERT: 5 107 ILE cc_start: 0.7952 (mm) cc_final: 0.7599 (pt) REVERT: 5 224 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7961 (tm-30) REVERT: 5 240 MET cc_start: 0.7461 (ptp) cc_final: 0.7162 (ptm) REVERT: 1 421 GLU cc_start: 0.8073 (tt0) cc_final: 0.7600 (tt0) REVERT: 1 462 TRP cc_start: 0.7514 (m100) cc_final: 0.7200 (m100) REVERT: 1 469 MET cc_start: 0.6710 (mmm) cc_final: 0.6497 (mmt) REVERT: 1 515 GLU cc_start: 0.5165 (mm-30) cc_final: 0.4581 (tp30) outliers start: 13 outliers final: 2 residues processed: 380 average time/residue: 0.3634 time to fit residues: 199.3836 Evaluate side-chains 193 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 18 GLN 4 92 GLN 4 177 GLN 4 210 GLN 4 220 ASN 4 244 ASN 4 320 ASN 3 180 ASN 3 317 GLN 2 96 ASN 2 128 ASN 2 236 GLN 2 288 ASN 2 352 GLN 5 18 HIS 5 19 ASN 5 104 ASN 5 244 ASN 1 477 ASN 1 534 GLN 1 620 HIS A 64 HIS A 83 ASN A 159 ASN B 24 GLN B 64 HIS B 159 ASN C 27 ASN C 64 HIS C 159 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.113168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.095853 restraints weight = 47579.379| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.83 r_work: 0.3330 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19543 Z= 0.171 Angle : 0.613 7.990 26607 Z= 0.322 Chirality : 0.042 0.167 3116 Planarity : 0.004 0.057 3280 Dihedral : 14.606 126.026 2963 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.28 % Allowed : 10.29 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2334 helix: 0.84 (0.15), residues: 1099 sheet: 0.47 (0.22), residues: 502 loop : -1.25 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 1 399 HIS 0.005 0.001 HIS 4 296 PHE 0.021 0.002 PHE B 19 TYR 0.024 0.002 TYR 2 64 ARG 0.006 0.001 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 1096) hydrogen bonds : angle 4.84972 ( 3077) covalent geometry : bond 0.00380 (19543) covalent geometry : angle 0.61274 (26607) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: 5 101 MET cc_start: 0.8086 (ptt) cc_final: 0.7369 (ptm) REVERT: 5 105 ASP cc_start: 0.7352 (m-30) cc_final: 0.6980 (m-30) REVERT: 5 107 ILE cc_start: 0.8131 (mm) cc_final: 0.7817 (pt) REVERT: 5 224 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8020 (tm-30) REVERT: 5 240 MET cc_start: 0.7392 (ptp) cc_final: 0.7127 (ptm) REVERT: 1 421 GLU cc_start: 0.7551 (tt0) cc_final: 0.7254 (tt0) REVERT: 1 515 GLU cc_start: 0.5069 (mm-30) cc_final: 0.4628 (tp30) REVERT: A 108 LYS cc_start: 0.8287 (tmtt) cc_final: 0.8082 (tmmt) REVERT: B 19 PHE cc_start: 0.7896 (m-80) cc_final: 0.7644 (m-10) REVERT: C 60 TYR cc_start: 0.7596 (t80) cc_final: 0.7302 (t80) outliers start: 26 outliers final: 9 residues processed: 209 average time/residue: 0.3033 time to fit residues: 97.6699 Evaluate side-chains 169 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 160 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 275 ILE Chi-restraints excluded: chain 5 residue 85 LEU Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 226 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 176 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: ** 2 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 141 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 HIS A 159 ASN C 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090438 restraints weight = 47553.298| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.82 r_work: 0.3228 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 19543 Z= 0.259 Angle : 0.700 7.502 26607 Z= 0.363 Chirality : 0.045 0.244 3116 Planarity : 0.005 0.060 3280 Dihedral : 14.674 126.052 2963 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.36 % Allowed : 12.06 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2334 helix: 0.70 (0.15), residues: 1087 sheet: 0.06 (0.22), residues: 526 loop : -1.16 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 295 HIS 0.009 0.002 HIS 2 124 PHE 0.026 0.002 PHE C 19 TYR 0.022 0.002 TYR 2 64 ARG 0.013 0.001 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.04587 ( 1096) hydrogen bonds : angle 4.92809 ( 3077) covalent geometry : bond 0.00596 (19543) covalent geometry : angle 0.69958 (26607) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 2.164 Fit side-chains REVERT: 5 107 ILE cc_start: 0.8113 (mm) cc_final: 0.7822 (pt) REVERT: 1 421 GLU cc_start: 0.7586 (tt0) cc_final: 0.7147 (tt0) REVERT: 1 515 GLU cc_start: 0.4685 (mm-30) cc_final: 0.4191 (tp30) REVERT: 1 594 ARG cc_start: 0.7150 (mtt180) cc_final: 0.6792 (mtt180) REVERT: A 51 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: A 80 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8012 (mtt180) REVERT: B 51 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: C 1 MET cc_start: 0.7184 (mtp) cc_final: 0.6774 (mtm) outliers start: 48 outliers final: 23 residues processed: 204 average time/residue: 0.3176 time to fit residues: 99.1478 Evaluate side-chains 171 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 2.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 93 ILE Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 3 residue 90 ILE Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 80 ASN Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 237 LEU Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 339 ILE Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 139 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 31 optimal weight: 0.1980 chunk 131 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 25 GLN 2 288 ASN 2 340 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 341 HIS C 83 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091928 restraints weight = 47472.543| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.83 r_work: 0.3253 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 19543 Z= 0.165 Angle : 0.570 7.451 26607 Z= 0.296 Chirality : 0.041 0.157 3116 Planarity : 0.004 0.057 3280 Dihedral : 14.403 130.403 2963 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.77 % Allowed : 14.43 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2334 helix: 1.00 (0.15), residues: 1092 sheet: 0.08 (0.22), residues: 522 loop : -1.06 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 324 HIS 0.003 0.001 HIS 5 18 PHE 0.015 0.001 PHE 1 443 TYR 0.017 0.001 TYR 4 71 ARG 0.007 0.001 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1096) hydrogen bonds : angle 4.67693 ( 3077) covalent geometry : bond 0.00380 (19543) covalent geometry : angle 0.57015 (26607) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 2.086 Fit side-chains REVERT: 2 140 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: 5 107 ILE cc_start: 0.8075 (mm) cc_final: 0.7777 (pt) REVERT: 1 421 GLU cc_start: 0.7547 (tt0) cc_final: 0.7104 (tt0) REVERT: 1 515 GLU cc_start: 0.4681 (mm-30) cc_final: 0.4204 (tp30) REVERT: 1 517 LYS cc_start: 0.6417 (tttt) cc_final: 0.5599 (mmmt) REVERT: 1 594 ARG cc_start: 0.7191 (mtt180) cc_final: 0.6826 (mtt180) REVERT: A 1 MET cc_start: 0.6926 (mtp) cc_final: 0.6593 (tpp) REVERT: A 80 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7975 (mtt180) REVERT: B 50 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8410 (tp) REVERT: B 51 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: B 224 ARG cc_start: 0.7296 (mtp85) cc_final: 0.7078 (mtp85) outliers start: 36 outliers final: 18 residues processed: 194 average time/residue: 0.3088 time to fit residues: 92.1629 Evaluate side-chains 171 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 25 GLN Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 140 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 25 GLN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091291 restraints weight = 47792.267| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.86 r_work: 0.3236 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19543 Z= 0.188 Angle : 0.589 8.677 26607 Z= 0.305 Chirality : 0.041 0.187 3116 Planarity : 0.004 0.057 3280 Dihedral : 14.368 133.038 2963 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.46 % Allowed : 14.48 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2334 helix: 1.06 (0.15), residues: 1093 sheet: 0.06 (0.22), residues: 526 loop : -1.04 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 2 27 HIS 0.004 0.001 HIS 2 124 PHE 0.020 0.002 PHE 2 280 TYR 0.015 0.001 TYR 4 71 ARG 0.008 0.001 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 1096) hydrogen bonds : angle 4.64809 ( 3077) covalent geometry : bond 0.00437 (19543) covalent geometry : angle 0.58949 (26607) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 2.201 Fit side-chains REVERT: 2 140 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: 5 107 ILE cc_start: 0.8105 (mm) cc_final: 0.7813 (pt) REVERT: 1 421 GLU cc_start: 0.7583 (tt0) cc_final: 0.7114 (tt0) REVERT: 1 517 LYS cc_start: 0.6419 (tttt) cc_final: 0.5591 (mmmt) REVERT: 1 594 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6859 (mtt180) REVERT: A 51 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 80 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8023 (mtt180) REVERT: B 50 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8426 (tp) REVERT: B 51 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7048 (tt0) REVERT: B 224 ARG cc_start: 0.7281 (mtp85) cc_final: 0.7051 (mtp85) REVERT: C 139 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8757 (pt) outliers start: 50 outliers final: 29 residues processed: 197 average time/residue: 0.3011 time to fit residues: 92.3568 Evaluate side-chains 187 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 140 ASP Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 51 THR Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain 1 residue 559 ILE Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 189 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 25 GLN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092751 restraints weight = 47543.079| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.83 r_work: 0.3261 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19543 Z= 0.122 Angle : 0.532 10.112 26607 Z= 0.275 Chirality : 0.040 0.244 3116 Planarity : 0.004 0.057 3280 Dihedral : 14.212 132.142 2963 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.87 % Allowed : 15.71 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2334 helix: 1.31 (0.16), residues: 1096 sheet: 0.12 (0.22), residues: 526 loop : -0.88 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 324 HIS 0.003 0.000 HIS 5 18 PHE 0.017 0.001 PHE 2 280 TYR 0.015 0.001 TYR 4 71 ARG 0.004 0.000 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 1096) hydrogen bonds : angle 4.46898 ( 3077) covalent geometry : bond 0.00275 (19543) covalent geometry : angle 0.53152 (26607) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 2.294 Fit side-chains REVERT: 5 107 ILE cc_start: 0.8099 (mm) cc_final: 0.7797 (pt) REVERT: 1 421 GLU cc_start: 0.7557 (tt0) cc_final: 0.7077 (tt0) REVERT: 1 517 LYS cc_start: 0.6345 (tttt) cc_final: 0.5556 (mmmt) REVERT: 1 594 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6846 (mtt180) REVERT: A 80 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8065 (mtt180) REVERT: B 1 MET cc_start: 0.7639 (mtm) cc_final: 0.7237 (mtt) REVERT: B 50 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8362 (tp) REVERT: B 51 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: B 224 ARG cc_start: 0.7296 (mtp85) cc_final: 0.7093 (mtp85) REVERT: C 7 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7776 (tp30) outliers start: 38 outliers final: 19 residues processed: 200 average time/residue: 0.3164 time to fit residues: 97.3350 Evaluate side-chains 186 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 194 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 86 optimal weight: 0.0030 chunk 129 optimal weight: 0.0970 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 55 optimal weight: 6.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 125 GLN ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094520 restraints weight = 47060.827| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.79 r_work: 0.3312 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19543 Z= 0.096 Angle : 0.499 9.660 26607 Z= 0.257 Chirality : 0.039 0.182 3116 Planarity : 0.004 0.056 3280 Dihedral : 13.903 128.849 2963 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.13 % Allowed : 16.49 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2334 helix: 1.61 (0.16), residues: 1098 sheet: 0.26 (0.22), residues: 526 loop : -0.74 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 4 11 HIS 0.003 0.000 HIS 5 18 PHE 0.019 0.001 PHE A 254 TYR 0.021 0.001 TYR 4 71 ARG 0.003 0.000 ARG 4 139 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 1096) hydrogen bonds : angle 4.27286 ( 3077) covalent geometry : bond 0.00205 (19543) covalent geometry : angle 0.49885 (26607) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 2.231 Fit side-chains REVERT: 3 205 MET cc_start: 0.7258 (tpp) cc_final: 0.7033 (mpp) REVERT: 5 107 ILE cc_start: 0.8092 (mm) cc_final: 0.7770 (pt) REVERT: 1 421 GLU cc_start: 0.7557 (tt0) cc_final: 0.7082 (tt0) REVERT: 1 489 LEU cc_start: 0.5738 (mp) cc_final: 0.5397 (mp) REVERT: A 114 TYR cc_start: 0.5860 (m-80) cc_final: 0.5651 (m-80) REVERT: A 150 ASP cc_start: 0.6779 (m-30) cc_final: 0.6519 (m-30) REVERT: B 50 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8361 (tp) REVERT: B 232 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8278 (tp30) REVERT: C 7 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7624 (tp30) REVERT: C 110 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7044 (mtp-110) outliers start: 23 outliers final: 14 residues processed: 206 average time/residue: 0.2986 time to fit residues: 95.8560 Evaluate side-chains 179 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 179 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092382 restraints weight = 47702.123| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.84 r_work: 0.3261 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19543 Z= 0.159 Angle : 0.556 9.691 26607 Z= 0.286 Chirality : 0.041 0.198 3116 Planarity : 0.004 0.058 3280 Dihedral : 14.018 133.115 2963 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.87 % Allowed : 16.30 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2334 helix: 1.53 (0.16), residues: 1099 sheet: 0.25 (0.22), residues: 526 loop : -0.76 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 324 HIS 0.004 0.001 HIS 4 232 PHE 0.018 0.002 PHE A 254 TYR 0.019 0.001 TYR 4 71 ARG 0.008 0.000 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1096) hydrogen bonds : angle 4.41343 ( 3077) covalent geometry : bond 0.00370 (19543) covalent geometry : angle 0.55608 (26607) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 2.424 Fit side-chains REVERT: 5 107 ILE cc_start: 0.8145 (mm) cc_final: 0.7859 (pt) REVERT: 1 421 GLU cc_start: 0.7521 (tt0) cc_final: 0.7070 (tt0) REVERT: 1 594 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6817 (mtt180) REVERT: A 80 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8047 (mtt180) REVERT: B 50 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8374 (tp) outliers start: 38 outliers final: 28 residues processed: 183 average time/residue: 0.3093 time to fit residues: 87.7414 Evaluate side-chains 184 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 5 residue 85 LEU Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 321 ILE Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain 1 residue 559 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 179 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 104 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092392 restraints weight = 47483.281| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.82 r_work: 0.3259 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19543 Z= 0.146 Angle : 0.547 9.670 26607 Z= 0.281 Chirality : 0.041 0.239 3116 Planarity : 0.004 0.057 3280 Dihedral : 13.999 132.875 2963 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.07 % Allowed : 16.15 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2334 helix: 1.50 (0.16), residues: 1096 sheet: 0.24 (0.22), residues: 526 loop : -0.75 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 399 HIS 0.004 0.001 HIS 4 232 PHE 0.017 0.001 PHE B 19 TYR 0.022 0.001 TYR 4 71 ARG 0.007 0.000 ARG 3 132 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 1096) hydrogen bonds : angle 4.41163 ( 3077) covalent geometry : bond 0.00337 (19543) covalent geometry : angle 0.54746 (26607) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 2.170 Fit side-chains REVERT: 3 205 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6662 (tpp) REVERT: 5 107 ILE cc_start: 0.8127 (mm) cc_final: 0.7853 (pt) REVERT: 1 421 GLU cc_start: 0.7537 (tt0) cc_final: 0.7077 (tt0) REVERT: 1 594 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6775 (mtt180) REVERT: A 80 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8071 (mtt180) REVERT: B 50 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8328 (tp) outliers start: 42 outliers final: 34 residues processed: 186 average time/residue: 0.2975 time to fit residues: 87.0150 Evaluate side-chains 191 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 4 residue 264 ILE Chi-restraints excluded: chain 3 residue 205 MET Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 49 LEU Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 5 residue 88 VAL Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 248 LEU Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 321 ILE Chi-restraints excluded: chain 5 residue 323 GLU Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain 1 residue 526 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 41 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 223 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 105 GLN ** 2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093781 restraints weight = 47296.520| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.82 r_work: 0.3295 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 19543 Z= 0.104 Angle : 0.514 9.684 26607 Z= 0.265 Chirality : 0.040 0.228 3116 Planarity : 0.004 0.056 3280 Dihedral : 13.852 130.912 2963 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.43 % Allowed : 17.09 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2334 helix: 1.63 (0.16), residues: 1100 sheet: 0.36 (0.22), residues: 522 loop : -0.62 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 324 HIS 0.003 0.000 HIS 5 18 PHE 0.018 0.001 PHE A 254 TYR 0.022 0.001 TYR 4 71 ARG 0.004 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 1096) hydrogen bonds : angle 4.31892 ( 3077) covalent geometry : bond 0.00231 (19543) covalent geometry : angle 0.51449 (26607) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 2.740 Fit side-chains REVERT: 3 205 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6551 (tpp) REVERT: 2 116 LEU cc_start: 0.9321 (mt) cc_final: 0.9112 (mt) REVERT: 5 107 ILE cc_start: 0.8116 (mm) cc_final: 0.7876 (pt) REVERT: 1 421 GLU cc_start: 0.7550 (tt0) cc_final: 0.7053 (tt0) REVERT: 1 473 MET cc_start: 0.7760 (mtp) cc_final: 0.7545 (mtt) REVERT: 1 489 LEU cc_start: 0.5770 (mp) cc_final: 0.5376 (mp) REVERT: 1 592 GLN cc_start: 0.5513 (tt0) cc_final: 0.5135 (tt0) REVERT: 1 594 ARG cc_start: 0.7149 (mtt180) cc_final: 0.6744 (mtt180) REVERT: A 80 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8007 (mtt180) REVERT: A 150 ASP cc_start: 0.6967 (m-30) cc_final: 0.6686 (m-30) REVERT: B 1 MET cc_start: 0.7809 (mtm) cc_final: 0.7362 (mtt) REVERT: B 50 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8310 (tp) REVERT: B 51 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: C 110 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7037 (mtp-110) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 0.3184 time to fit residues: 93.2491 Evaluate side-chains 179 residues out of total 2110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 67 LEU Chi-restraints excluded: chain 4 residue 131 MET Chi-restraints excluded: chain 4 residue 236 VAL Chi-restraints excluded: chain 3 residue 205 MET Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 2 residue 103 ILE Chi-restraints excluded: chain 2 residue 245 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 5 residue 149 ASP Chi-restraints excluded: chain 5 residue 308 LEU Chi-restraints excluded: chain 5 residue 316 THR Chi-restraints excluded: chain 5 residue 349 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 144 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 208 ASN ** 3 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.108951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091492 restraints weight = 47946.107| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.85 r_work: 0.3233 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 19543 Z= 0.218 Angle : 0.616 9.923 26607 Z= 0.315 Chirality : 0.043 0.258 3116 Planarity : 0.004 0.058 3280 Dihedral : 14.092 136.079 2963 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.12 % Allowed : 16.64 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2334 helix: 1.32 (0.16), residues: 1096 sheet: 0.19 (0.22), residues: 532 loop : -0.80 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 5 259 HIS 0.010 0.001 HIS 4 232 PHE 0.018 0.002 PHE 1 443 TYR 0.023 0.002 TYR 4 71 ARG 0.009 0.001 ARG 2 107 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 1096) hydrogen bonds : angle 4.56983 ( 3077) covalent geometry : bond 0.00510 (19543) covalent geometry : angle 0.61642 (26607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11143.60 seconds wall clock time: 192 minutes 53.24 seconds (11573.24 seconds total)