Starting phenix.real_space_refine on Sun Aug 24 06:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw7_41661/08_2025/8tw7_41661.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw7_41661/08_2025/8tw7_41661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tw7_41661/08_2025/8tw7_41661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw7_41661/08_2025/8tw7_41661.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tw7_41661/08_2025/8tw7_41661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw7_41661/08_2025/8tw7_41661.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 83 5.16 5 C 11570 2.51 5 N 3101 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18337 Number of models: 1 Model: "" Number of chains: 12 Chain: "5" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2606 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2409 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 36 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: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2655 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "1" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2005 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 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: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Time building chain proxies: 5.02, per 1000 atoms: 0.27 Number of scatterers: 18337 At special positions: 0 Unit cell: (123.372, 114.264, 147.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 11 15.00 Mg 3 11.99 O 3569 8.00 N 3101 7.00 C 11570 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 883.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 14 sheets defined 53.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain '5' and resid 19 through 32 removed outlier: 4.418A pdb=" N GLN 5 32 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 61 Processing helix chain '5' and resid 62 through 66 removed outlier: 3.516A pdb=" N VAL 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR 5 66 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 62 through 66' Processing helix chain '5' and resid 97 through 101 removed outlier: 3.964A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 117 removed outlier: 3.691A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 146 Processing helix chain '5' and resid 147 through 161 removed outlier: 4.060A pdb=" N ARG 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR 5 157 " --> pdb=" O ALA 5 153 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.579A 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: 4.020A 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: 3.655A pdb=" N GLU 5 281 " --> pdb=" O ASN 5 277 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 335 Processing helix chain '5' and resid 337 through 353 removed outlier: 3.737A 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 '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.599A pdb=" N ILE 4 23 " --> pdb=" O LEU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 40 Processing helix chain '4' and resid 55 through 68 Processing helix chain '4' and resid 70 through 74 Processing helix chain '4' and resid 85 through 99 removed outlier: 4.071A pdb=" N ILE 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 119 Processing helix chain '4' and resid 120 through 134 removed outlier: 3.781A pdb=" N ARG 4 128 " --> pdb=" O GLN 4 124 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG 4 129 " --> pdb=" O GLN 4 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 4 130 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR 4 134 " --> pdb=" O THR 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 150 Processing helix chain '4' and resid 151 through 157 removed outlier: 3.677A pdb=" N ARG 4 157 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 183 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 201 through 217 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 232 through 241 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: 3.726A 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: 3.519A pdb=" N THR 3 36 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 72 Processing helix chain '3' and resid 74 through 78 removed outlier: 3.513A pdb=" N MET 3 78 " --> pdb=" O ASN 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 89 through 103 removed outlier: 4.013A pdb=" N LYS 3 98 " --> pdb=" O ARG 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 122 removed outlier: 3.549A pdb=" N ALA 3 121 " --> pdb=" O GLU 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 137 removed outlier: 4.379A pdb=" N ARG 3 132 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 3.682A 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: 3.552A 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 removed outlier: 3.555A pdb=" N GLY 3 237 " --> pdb=" O TYR 3 233 " (cutoff:3.500A) Processing helix chain '3' and resid 240 through 253 Processing helix chain '3' and resid 255 through 270 removed outlier: 3.801A pdb=" N LYS 3 270 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 286 Processing helix chain '3' and resid 293 through 311 Processing helix chain '3' and resid 315 through 332 Processing helix chain '2' and resid 15 through 24 Processing helix chain '2' and resid 26 through 31 Processing helix chain '2' and resid 42 through 55 removed outlier: 3.620A pdb=" N VAL 2 46 " --> pdb=" O GLN 2 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 48 " --> pdb=" O HIS 2 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 88 Proline residue: 2 85 - end of helix Processing helix chain '2' and resid 102 through 116 removed outlier: 3.894A pdb=" N VAL 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 2 111 " --> pdb=" O ARG 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 129 removed outlier: 3.635A pdb=" N LEU 2 126 " --> pdb=" O SER 2 122 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.759A pdb=" N ARG 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR 2 156 " --> pdb=" O ALA 2 152 " (cutoff:3.500A) removed outlier: 3.544A 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: 5.161A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG 2 200 " --> pdb=" O ASN 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 225 Processing helix chain '2' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU 2 245 " --> pdb=" O GLY 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 260 removed outlier: 3.581A pdb=" N LEU 2 259 " --> pdb=" O GLN 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 265 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 '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: 3.639A 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: 3.975A pdb=" N TYR 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 1 475 " --> pdb=" O GLN 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 479 No H-bonds generated for 'chain '1' and resid 477 through 479' Processing helix chain '1' and resid 480 through 485 removed outlier: 3.859A pdb=" N SER 1 484 " --> pdb=" O LEU 1 480 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 1 485 " --> pdb=" O LEU 1 481 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 485' Processing helix chain '1' and resid 485 through 496 removed outlier: 3.873A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE 1 491 " --> pdb=" O VAL 1 487 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 1 492 " --> pdb=" O PRO 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 534 removed outlier: 3.656A pdb=" N GLU 1 512 " --> pdb=" O ASN 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 542 removed outlier: 3.765A pdb=" N PHE 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 550 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.558A pdb=" N TYR 1 554 " --> pdb=" O GLU 1 550 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 566 Processing helix chain '1' and resid 568 through 586 Processing helix chain '1' and resid 610 through 615 Processing helix chain '1' and resid 617 through 643 removed outlier: 3.675A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.310A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.110A pdb=" N GLN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.656A 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: 4.107A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.308A 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: 4.107A 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 '5' and resid 69 through 76 removed outlier: 6.876A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN 5 141 " --> pdb=" O LEU 5 94 " (cutoff:3.500A) removed outlier: 6.938A 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: 7.984A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 136 " (cutoff:3.500A) removed outlier: 6.439A 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=AA2, 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=AA2 Processing sheet with id=AA3, 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: 7.467A pdb=" N ALA 4 141 " --> pdb=" O LYS 4 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE 4 46 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA4 Processing sheet with id=AA5, first strand: chain '3' and resid 79 through 82 removed outlier: 6.603A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA 3 147 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) removed outlier: 6.279A 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=AA6, first strand: chain '2' and resid 92 through 95 removed outlier: 6.221A pdb=" N LEU 2 62 " --> pdb=" O PHE 2 187 " (cutoff:3.500A) Processing sheet with id=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: 3.522A pdb=" N GLU A 59 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU A 25 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 40 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 240 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 7.067A 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: 6.290A pdb=" N SER A 157 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP A 172 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 177 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 181 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 111 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 59 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 172 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 157 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU B 25 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.446A 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: 4.662A 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: 5.539A pdb=" N LEU C 25 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL C 40 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.698A 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) 1063 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.27 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: 3147 1.26 - 1.43: 4426 1.43 - 1.61: 10919 1.61 - 1.78: 11 1.78 - 1.95: 119 Bond restraints: 18622 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 4.95e+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 4.89e+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 4.82e+01 bond pdb=" C GLU A 258 " pdb=" O GLU A 258 " ideal model delta sigma weight residual 1.231 1.370 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C4 ADP 5 401 " pdb=" C5 ADP 5 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 18617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 24372 3.06 - 6.12: 757 6.12 - 9.19: 68 9.19 - 12.25: 9 12.25 - 15.31: 7 Bond angle restraints: 25213 Sorted by residual: 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 GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 110.41 122.83 -12.42 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 113.72 104.56 9.16 1.30e+00 5.92e-01 4.97e+01 angle pdb=" N ASP C 97 " pdb=" CA ASP C 97 " pdb=" C ASP C 97 " ideal model delta sigma weight residual 113.72 104.58 9.14 1.30e+00 5.92e-01 4.94e+01 angle pdb=" N ASP A 97 " pdb=" CA ASP A 97 " pdb=" C ASP A 97 " ideal model delta sigma weight residual 113.72 104.71 9.01 1.30e+00 5.92e-01 4.80e+01 ... (remaining 25208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.35: 10938 26.35 - 52.69: 442 52.69 - 79.04: 65 79.04 - 105.38: 18 105.38 - 131.73: 3 Dihedral angle restraints: 11466 sinusoidal: 4599 harmonic: 6867 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 300.00 168.27 131.73 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 60.68 -120.68 1 2.00e+01 2.50e-03 3.62e+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 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.30e+01 ... (remaining 11463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2571 0.119 - 0.238: 310 0.238 - 0.357: 63 0.357 - 0.476: 12 0.476 - 0.595: 5 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+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 8.76e+00 chirality pdb=" CA CYS C 22 " pdb=" N CYS C 22 " pdb=" C CYS C 22 " pdb=" CB CYS C 22 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 2958 not shown) Planarity restraints: 3227 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 8.16e-02 6.66e+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 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 563 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 563 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 563 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE 1 563 " -0.081 2.00e-02 2.50e+03 ... (remaining 3224 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 20 2.33 - 2.97: 8745 2.97 - 3.61: 26477 3.61 - 4.26: 41430 4.26 - 4.90: 69770 Nonbonded interactions: 146442 Sorted by model distance: nonbonded pdb=" CD1 LEU 5 242 " pdb=" CG MET 1 558 " model vdw 1.684 3.860 nonbonded pdb=" O ASP A 109 " pdb=" O ILE B 181 " model vdw 1.772 3.040 nonbonded pdb=" CB ALA 2 297 " pdb=" OE1 GLU 2 339 " model vdw 2.094 3.460 nonbonded pdb=" O3G AGS 3 401 " pdb="MG MG 3 402 " model vdw 2.104 2.170 nonbonded pdb=" OD1 ASP 3 229 " pdb=" OD1 ASP 3 230 " model vdw 2.122 3.040 ... (remaining 146437 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.370 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 0.336 18623 Z= 0.571 Angle : 1.207 15.312 25213 Z= 0.783 Chirality : 0.088 0.595 2961 Planarity : 0.009 0.184 3227 Dihedral : 14.636 131.731 6986 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.95 % Allowed : 3.53 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 6.66 % Favored : 92.79 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.16), residues: 2324 helix: -0.45 (0.14), residues: 1099 sheet: 0.11 (0.22), residues: 505 loop : -1.87 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG B 224 TYR 0.078 0.007 TYR A 133 PHE 0.087 0.010 PHE 1 563 TRP 0.037 0.003 TRP 1 399 HIS 0.045 0.002 HIS 4 232 Details of bonding type rmsd covalent geometry : bond 0.00875 (18622) covalent geometry : angle 1.20721 (25213) hydrogen bonds : bond 0.15447 ( 1063) hydrogen bonds : angle 6.40307 ( 3009) Misc. bond : bond 0.33567 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 96 ILE cc_start: 0.9412 (mp) cc_final: 0.9171 (mt) REVERT: 4 45 MET cc_start: 0.8985 (ptp) cc_final: 0.8783 (ptp) REVERT: 4 202 MET cc_start: 0.8928 (tpp) cc_final: 0.8301 (tpp) REVERT: 2 291 MET cc_start: 0.8918 (mmm) cc_final: 0.8717 (mmm) REVERT: 2 345 ASN cc_start: 0.8747 (t0) cc_final: 0.8383 (t0) REVERT: 1 420 TYR cc_start: 0.8481 (t80) cc_final: 0.8156 (t80) REVERT: B 45 VAL cc_start: 0.9434 (m) cc_final: 0.9136 (t) outliers start: 11 outliers final: 1 residues processed: 211 average time/residue: 0.1781 time to fit residues: 54.4533 Evaluate side-chains 117 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 80 ASN 5 104 ASN 5 244 ASN 5 341 HIS 4 18 GLN ** 4 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 92 GLN 4 177 GLN 4 232 HIS 4 244 ASN 4 320 ASN 3 317 GLN 2 128 ASN 2 236 GLN ** 2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 GLN 1 534 GLN 1 620 HIS A 159 ASN B 159 ASN C 64 HIS C 83 ASN C 159 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.073126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.064989 restraints weight = 64444.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.066007 restraints weight = 39304.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.066976 restraints weight = 24809.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.066939 restraints weight = 20019.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067062 restraints weight = 17610.833| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18623 Z= 0.167 Angle : 0.588 8.502 25213 Z= 0.304 Chirality : 0.042 0.236 2961 Planarity : 0.004 0.054 3227 Dihedral : 7.617 130.158 2564 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 1.09 % Allowed : 8.95 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.17), residues: 2324 helix: 0.87 (0.15), residues: 1111 sheet: 0.54 (0.22), residues: 498 loop : -1.39 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 4 285 TYR 0.024 0.002 TYR A 211 PHE 0.021 0.002 PHE 1 443 TRP 0.013 0.002 TRP 1 399 HIS 0.008 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00368 (18622) covalent geometry : angle 0.58755 (25213) hydrogen bonds : bond 0.03977 ( 1063) hydrogen bonds : angle 4.91925 ( 3009) Misc. bond : bond 0.00680 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 96 ILE cc_start: 0.9226 (mp) cc_final: 0.8914 (mt) REVERT: 4 202 MET cc_start: 0.9057 (tpp) cc_final: 0.8208 (tpp) REVERT: 1 420 TYR cc_start: 0.8555 (t80) cc_final: 0.8218 (t80) REVERT: B 45 VAL cc_start: 0.9146 (m) cc_final: 0.8849 (t) REVERT: B 51 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.7334 (tt0) outliers start: 22 outliers final: 7 residues processed: 135 average time/residue: 0.1636 time to fit residues: 33.0283 Evaluate side-chains 112 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 104 ASN Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain B residue 51 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 227 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 chunk 187 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 288 ASN ** C 94 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 = 0.2974 r_free = 0.2974 target = 0.072846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.064679 restraints weight = 65531.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.065708 restraints weight = 35900.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.066362 restraints weight = 23807.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.066332 restraints weight = 20274.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.066601 restraints weight = 18574.608| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18623 Z= 0.116 Angle : 0.493 7.523 25213 Z= 0.255 Chirality : 0.040 0.210 2961 Planarity : 0.003 0.054 3227 Dihedral : 7.022 124.902 2561 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.09 % Allowed : 9.79 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2324 helix: 1.26 (0.16), residues: 1117 sheet: 0.42 (0.22), residues: 508 loop : -1.22 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 184 TYR 0.015 0.001 TYR A 211 PHE 0.017 0.001 PHE 1 443 TRP 0.010 0.001 TRP 5 259 HIS 0.003 0.001 HIS 5 18 Details of bonding type rmsd covalent geometry : bond 0.00250 (18622) covalent geometry : angle 0.49303 (25213) hydrogen bonds : bond 0.03447 ( 1063) hydrogen bonds : angle 4.57263 ( 3009) Misc. bond : bond 0.00130 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.9029 (tpp) cc_final: 0.8162 (tpp) REVERT: 3 299 LEU cc_start: 0.9435 (tp) cc_final: 0.9213 (tp) REVERT: 1 420 TYR cc_start: 0.8600 (t80) cc_final: 0.8288 (t80) REVERT: A 51 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8553 (tm-30) REVERT: C 7 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8315 (tp30) outliers start: 22 outliers final: 8 residues processed: 134 average time/residue: 0.1675 time to fit residues: 33.6632 Evaluate side-chains 118 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 194 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 219 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 GLN 4 208 ASN 2 313 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.069289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.060898 restraints weight = 66779.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.061727 restraints weight = 37131.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.062515 restraints weight = 27149.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.062622 restraints weight = 19709.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.062685 restraints weight = 19359.375| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18623 Z= 0.198 Angle : 0.555 9.392 25213 Z= 0.284 Chirality : 0.041 0.196 2961 Planarity : 0.004 0.054 3227 Dihedral : 6.667 124.504 2561 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 1.34 % Allowed : 11.18 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2324 helix: 1.39 (0.16), residues: 1100 sheet: 0.51 (0.23), residues: 505 loop : -1.11 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 5 184 TYR 0.015 0.002 TYR A 211 PHE 0.020 0.002 PHE 1 443 TRP 0.013 0.002 TRP 5 259 HIS 0.008 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00450 (18622) covalent geometry : angle 0.55543 (25213) hydrogen bonds : bond 0.03589 ( 1063) hydrogen bonds : angle 4.61493 ( 3009) Misc. bond : bond 0.00159 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.9022 (tpp) cc_final: 0.8086 (tpp) REVERT: 2 71 LYS cc_start: 0.8338 (mtmm) cc_final: 0.7761 (ptpp) REVERT: 1 420 TYR cc_start: 0.8741 (t80) cc_final: 0.8377 (t80) REVERT: A 7 GLU cc_start: 0.9478 (OUTLIER) cc_final: 0.7492 (tp30) REVERT: A 51 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: B 51 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.7632 (tt0) outliers start: 27 outliers final: 13 residues processed: 130 average time/residue: 0.1575 time to fit residues: 31.2778 Evaluate side-chains 119 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 591 ILE Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 48 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 19 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 124 HIS 2 128 ASN 2 265 HIS ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.068032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.059743 restraints weight = 67086.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.060543 restraints weight = 37761.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.061383 restraints weight = 27357.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061413 restraints weight = 20005.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.061514 restraints weight = 19412.409| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18623 Z= 0.216 Angle : 0.555 7.287 25213 Z= 0.286 Chirality : 0.042 0.201 2961 Planarity : 0.004 0.053 3227 Dihedral : 6.442 122.719 2561 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.48 % Favored : 95.48 % Rotamer: Outliers : 1.64 % Allowed : 11.43 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.18), residues: 2324 helix: 1.32 (0.16), residues: 1095 sheet: 0.48 (0.23), residues: 505 loop : -1.08 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 3 206 TYR 0.013 0.002 TYR A 211 PHE 0.019 0.002 PHE 1 443 TRP 0.014 0.002 TRP 5 259 HIS 0.009 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00497 (18622) covalent geometry : angle 0.55457 (25213) hydrogen bonds : bond 0.03737 ( 1063) hydrogen bonds : angle 4.70899 ( 3009) Misc. bond : bond 0.00183 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8976 (tpp) cc_final: 0.8744 (tpp) REVERT: 2 71 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7742 (ptpp) REVERT: 2 172 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: A 7 GLU cc_start: 0.9480 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: A 51 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: B 51 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: C 7 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.8596 (tp30) outliers start: 33 outliers final: 17 residues processed: 128 average time/residue: 0.1622 time to fit residues: 31.5443 Evaluate side-chains 121 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 96 ILE Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 300 VAL Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 591 ILE Chi-restraints excluded: chain 1 residue 639 ILE Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 53 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 181 optimal weight: 0.0370 chunk 162 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 160 optimal weight: 0.0670 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 125 GLN 4 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.070586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.062611 restraints weight = 65519.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.063532 restraints weight = 35909.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.064091 restraints weight = 24157.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.064083 restraints weight = 20367.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.064351 restraints weight = 19096.866| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18623 Z= 0.092 Angle : 0.460 6.337 25213 Z= 0.237 Chirality : 0.039 0.144 2961 Planarity : 0.003 0.053 3227 Dihedral : 6.258 123.727 2561 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 1.19 % Allowed : 12.18 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.18), residues: 2324 helix: 1.62 (0.16), residues: 1102 sheet: 0.54 (0.23), residues: 505 loop : -0.88 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 69 TYR 0.009 0.001 TYR B 211 PHE 0.015 0.001 PHE 1 443 TRP 0.011 0.001 TRP 1 399 HIS 0.011 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00189 (18622) covalent geometry : angle 0.45959 (25213) hydrogen bonds : bond 0.02995 ( 1063) hydrogen bonds : angle 4.38962 ( 3009) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8932 (tpp) cc_final: 0.8041 (tpp) REVERT: 4 307 LEU cc_start: 0.9532 (tp) cc_final: 0.9298 (tp) REVERT: 3 205 MET cc_start: 0.9256 (mmt) cc_final: 0.8761 (mmt) REVERT: 3 299 LEU cc_start: 0.9400 (tp) cc_final: 0.9121 (tt) REVERT: 2 71 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7450 (ptpp) REVERT: 2 172 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.8007 (m-80) REVERT: 1 420 TYR cc_start: 0.8689 (t80) cc_final: 0.8337 (t80) REVERT: A 7 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: A 51 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: B 51 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: C 7 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8542 (tp30) outliers start: 24 outliers final: 10 residues processed: 130 average time/residue: 0.1567 time to fit residues: 30.9334 Evaluate side-chains 121 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 227 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 207 optimal weight: 30.0000 chunk 148 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN ** C 94 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 = 0.2886 r_free = 0.2886 target = 0.068736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.060476 restraints weight = 66827.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061299 restraints weight = 37136.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.062098 restraints weight = 26942.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.062119 restraints weight = 19721.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.062308 restraints weight = 19023.889| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18623 Z= 0.177 Angle : 0.516 6.788 25213 Z= 0.263 Chirality : 0.040 0.156 2961 Planarity : 0.004 0.051 3227 Dihedral : 6.122 122.224 2561 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.09 % Favored : 95.87 % Rotamer: Outliers : 1.39 % Allowed : 12.38 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 2324 helix: 1.58 (0.16), residues: 1102 sheet: 0.52 (0.23), residues: 493 loop : -0.93 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 4 69 TYR 0.011 0.001 TYR 2 286 PHE 0.020 0.002 PHE 1 443 TRP 0.012 0.001 TRP 5 259 HIS 0.011 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00408 (18622) covalent geometry : angle 0.51593 (25213) hydrogen bonds : bond 0.03387 ( 1063) hydrogen bonds : angle 4.49787 ( 3009) Misc. bond : bond 0.00135 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8938 (tpp) cc_final: 0.8726 (tpp) REVERT: 3 205 MET cc_start: 0.9285 (mmt) cc_final: 0.8680 (mmt) REVERT: 2 71 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7775 (ptpp) REVERT: 2 172 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: 1 420 TYR cc_start: 0.8757 (t80) cc_final: 0.8422 (t80) REVERT: 1 577 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: A 7 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: A 51 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7227 (tm-30) REVERT: B 51 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: C 7 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8562 (tp30) outliers start: 28 outliers final: 14 residues processed: 124 average time/residue: 0.1546 time to fit residues: 29.2941 Evaluate side-chains 123 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 300 VAL Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 166 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 35 optimal weight: 5.9990 chunk 188 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.068809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.060973 restraints weight = 66834.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.061846 restraints weight = 36119.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.062883 restraints weight = 24015.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.062803 restraints weight = 18987.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.062972 restraints weight = 16201.528| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18623 Z= 0.161 Angle : 0.501 7.453 25213 Z= 0.257 Chirality : 0.040 0.161 2961 Planarity : 0.003 0.051 3227 Dihedral : 6.104 122.445 2561 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.34 % Allowed : 12.72 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2324 helix: 1.55 (0.16), residues: 1105 sheet: 0.38 (0.23), residues: 503 loop : -0.90 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 69 TYR 0.010 0.001 TYR 2 286 PHE 0.019 0.001 PHE 1 443 TRP 0.012 0.001 TRP 5 259 HIS 0.011 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00367 (18622) covalent geometry : angle 0.50076 (25213) hydrogen bonds : bond 0.03341 ( 1063) hydrogen bonds : angle 4.49842 ( 3009) Misc. bond : bond 0.00116 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 71 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7752 (ptpp) REVERT: 2 172 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: 1 420 TYR cc_start: 0.8730 (t80) cc_final: 0.8372 (t80) REVERT: 1 577 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 7 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: A 51 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: B 51 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: B 224 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8142 (mtp85) REVERT: C 7 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8565 (tp30) outliers start: 27 outliers final: 13 residues processed: 124 average time/residue: 0.1574 time to fit residues: 29.9342 Evaluate side-chains 122 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 2 residue 300 VAL Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 62 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.068868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.060329 restraints weight = 66725.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.061498 restraints weight = 38855.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.062211 restraints weight = 26022.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.062836 restraints weight = 19544.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.063168 restraints weight = 15558.069| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18623 Z= 0.138 Angle : 0.489 6.495 25213 Z= 0.250 Chirality : 0.040 0.180 2961 Planarity : 0.003 0.050 3227 Dihedral : 6.015 122.361 2561 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 1.14 % Allowed : 12.97 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2324 helix: 1.65 (0.16), residues: 1100 sheet: 0.38 (0.23), residues: 503 loop : -0.86 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 52 TYR 0.013 0.001 TYR 5 42 PHE 0.018 0.001 PHE 1 443 TRP 0.010 0.001 TRP 5 259 HIS 0.012 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00311 (18622) covalent geometry : angle 0.48862 (25213) hydrogen bonds : bond 0.03229 ( 1063) hydrogen bonds : angle 4.45556 ( 3009) Misc. bond : bond 0.00110 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: 3 299 LEU cc_start: 0.9417 (tp) cc_final: 0.9211 (tp) REVERT: 2 71 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7762 (ptpp) REVERT: 2 172 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: 1 420 TYR cc_start: 0.8739 (t80) cc_final: 0.8370 (t80) REVERT: 1 577 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: A 7 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: A 51 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: B 51 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 7 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8556 (tp30) outliers start: 23 outliers final: 14 residues processed: 120 average time/residue: 0.1565 time to fit residues: 28.8894 Evaluate side-chains 120 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.068997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.060473 restraints weight = 66725.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.061671 restraints weight = 38528.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.062496 restraints weight = 25714.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.063033 restraints weight = 18959.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.063339 restraints weight = 15254.519| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18623 Z= 0.129 Angle : 0.487 8.025 25213 Z= 0.248 Chirality : 0.040 0.173 2961 Planarity : 0.003 0.050 3227 Dihedral : 5.988 122.400 2561 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 0.94 % Allowed : 13.42 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 2324 helix: 1.69 (0.16), residues: 1100 sheet: 0.40 (0.23), residues: 503 loop : -0.85 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 69 TYR 0.011 0.001 TYR 5 42 PHE 0.018 0.001 PHE 1 443 TRP 0.010 0.001 TRP 5 259 HIS 0.015 0.001 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.00291 (18622) covalent geometry : angle 0.48675 (25213) hydrogen bonds : bond 0.03177 ( 1063) hydrogen bonds : angle 4.42522 ( 3009) Misc. bond : bond 0.00099 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: 3 205 MET cc_start: 0.9280 (mmt) cc_final: 0.8845 (mmt) REVERT: 3 299 LEU cc_start: 0.9416 (tp) cc_final: 0.9145 (tt) REVERT: 2 71 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7781 (ptpp) REVERT: 2 172 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: 1 420 TYR cc_start: 0.8728 (t80) cc_final: 0.8367 (t80) REVERT: 1 577 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: A 7 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: A 51 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: B 51 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: C 7 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8543 (tp30) outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.1574 time to fit residues: 28.4334 Evaluate side-chains 120 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 105 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 0.0970 chunk 100 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN B 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.068754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.060229 restraints weight = 67359.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.061440 restraints weight = 38839.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.062265 restraints weight = 25971.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.062787 restraints weight = 19193.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.063100 restraints weight = 15438.158| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18623 Z= 0.143 Angle : 0.491 7.146 25213 Z= 0.251 Chirality : 0.040 0.171 2961 Planarity : 0.003 0.049 3227 Dihedral : 5.966 122.197 2561 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 1.14 % Allowed : 13.42 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.18), residues: 2324 helix: 1.68 (0.16), residues: 1100 sheet: 0.41 (0.23), residues: 503 loop : -0.84 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 52 TYR 0.011 0.001 TYR 5 42 PHE 0.018 0.001 PHE 1 443 TRP 0.011 0.001 TRP 5 259 HIS 0.006 0.001 HIS 5 18 Details of bonding type rmsd covalent geometry : bond 0.00324 (18622) covalent geometry : angle 0.49112 (25213) hydrogen bonds : bond 0.03226 ( 1063) hydrogen bonds : angle 4.44532 ( 3009) Misc. bond : bond 0.00103 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.11 seconds wall clock time: 43 minutes 39.30 seconds (2619.30 seconds total)