Starting phenix.real_space_refine on Sun Oct 13 03:32:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/10_2024/7tfl_25876.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/10_2024/7tfl_25876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/10_2024/7tfl_25876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/10_2024/7tfl_25876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/10_2024/7tfl_25876.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfl_25876/10_2024/7tfl_25876.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 209 atoms to isotropic. 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 38 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 8526 2.51 5 N 2397 2.21 5 O 2657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 13690 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2659 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain breaks: 2 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2581 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2684 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "I" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.25, per 1000 atoms: 0.68 Number of scatterers: 13690 At special positions: 0 Unit cell: (86.94, 119.232, 128.34, 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 68 16.00 P 38 15.00 Mg 4 11.99 O 2657 8.00 N 2397 7.00 C 8526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3142 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 7 sheets defined 64.9% alpha, 5.6% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 327 through 330 removed outlier: 3.541A pdb=" N SER A 330 " --> pdb=" O TRP A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 358 through 370 Processing helix chain 'A' and resid 426 through 430 removed outlier: 3.617A pdb=" N MET A 429 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 removed outlier: 3.563A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 513 through 528 removed outlier: 4.000A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.891A pdb=" N ALA A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 4.331A pdb=" N ARG A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.586A pdb=" N GLN A 593 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 609 through 632 removed outlier: 3.518A pdb=" N ASN A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.554A pdb=" N HIS A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 646 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 removed outlier: 4.056A pdb=" N VAL A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.604A pdb=" N SER A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 26 through 40 removed outlier: 3.964A pdb=" N ILE B 30 " --> pdb=" O ASN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 87 through 99 removed outlier: 3.648A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 151 through 158 removed outlier: 3.641A pdb=" N GLN B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.925A pdb=" N VAL B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.515A pdb=" N ALA B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.501A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 257 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.746A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 removed outlier: 3.519A pdb=" N TYR C 19 " --> pdb=" O TRP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.653A pdb=" N VAL C 27 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.513A pdb=" N THR C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 89 through 103 removed outlier: 4.102A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.654A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.689A pdb=" N LEU C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.628A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.146A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 removed outlier: 4.327A pdb=" N GLU C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 313 removed outlier: 3.534A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 removed outlier: 3.680A pdb=" N GLN C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.789A pdb=" N TYR D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 55 removed outlier: 4.028A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 102 through 116 removed outlier: 4.015A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 116 " --> pdb=" O ASN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.613A pdb=" N LEU D 126 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 127 " --> pdb=" O HIS D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 160 removed outlier: 4.304A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 removed outlier: 3.558A pdb=" N LEU D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.902A pdb=" N THR D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 334 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.051A pdb=" N LYS E 7 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 8' Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.035A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.090A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 149 through 161 removed outlier: 4.024A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 184 removed outlier: 3.583A pdb=" N LYS E 182 " --> pdb=" O ILE E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 209 removed outlier: 3.539A pdb=" N ILE E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.858A pdb=" N SER E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.606A pdb=" N LEU E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.842A pdb=" N ILE E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 334 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.148A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 424 removed outlier: 3.660A pdb=" N ILE A 473 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 352 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.072A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 80 through 82 removed outlier: 4.502A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE C 115 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 82 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.547A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.472A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP D 140 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D 95 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 61 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 168 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.910A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 83 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 139 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 4521 1.36 - 1.51: 3565 1.51 - 1.66: 5768 1.66 - 1.80: 61 1.80 - 1.95: 44 Bond restraints: 13959 Sorted by residual: bond pdb=" N ILE A 547 " pdb=" CA ILE A 547 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.12e+01 bond pdb=" N ASN A 546 " pdb=" CA ASN A 546 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N LEU A 549 " pdb=" CA LEU A 549 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N ALA A 548 " pdb=" CA ALA A 548 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.31e-02 5.83e+03 5.70e+00 bond pdb=" N LYS A 550 " pdb=" CA LYS A 550 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.22e+00 ... (remaining 13954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 18668 2.09 - 4.18: 275 4.18 - 6.27: 37 6.27 - 8.36: 10 8.36 - 10.46: 4 Bond angle restraints: 18994 Sorted by residual: angle pdb=" CA PRO C 239 " pdb=" N PRO C 239 " pdb=" CD PRO C 239 " ideal model delta sigma weight residual 112.00 105.95 6.05 1.40e+00 5.10e-01 1.87e+01 angle pdb=" N GLU C 279 " pdb=" CA GLU C 279 " pdb=" CB GLU C 279 " ideal model delta sigma weight residual 110.12 116.46 -6.34 1.47e+00 4.63e-01 1.86e+01 angle pdb=" C ILE B 151 " pdb=" N GLU B 152 " pdb=" CA GLU B 152 " ideal model delta sigma weight residual 120.09 125.11 -5.02 1.25e+00 6.40e-01 1.62e+01 angle pdb=" CA ILE A 547 " pdb=" C ILE A 547 " pdb=" O ILE A 547 " ideal model delta sigma weight residual 121.63 118.04 3.59 9.90e-01 1.02e+00 1.31e+01 angle pdb=" CB LYS D 111 " pdb=" CG LYS D 111 " pdb=" CD LYS D 111 " ideal model delta sigma weight residual 111.30 119.46 -8.16 2.30e+00 1.89e-01 1.26e+01 ... (remaining 18989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 8109 28.10 - 56.19: 403 56.19 - 84.29: 31 84.29 - 112.38: 1 112.38 - 140.48: 2 Dihedral angle restraints: 8546 sinusoidal: 3715 harmonic: 4831 Sorted by residual: dihedral pdb=" O1B ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PB ADP E 402 " pdb=" PA ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 -172.56 112.56 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" O1A AGS D 500 " pdb=" O3A AGS D 500 " pdb=" PA AGS D 500 " pdb=" PB AGS D 500 " ideal model delta sinusoidal sigma weight residual -67.73 72.75 -140.48 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA PHE A 346 " pdb=" C PHE A 346 " pdb=" N ARG A 347 " pdb=" CA ARG A 347 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 8543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1616 0.041 - 0.082: 464 0.082 - 0.123: 112 0.123 - 0.165: 12 0.165 - 0.206: 3 Chirality restraints: 2207 Sorted by residual: chirality pdb=" CG LEU B 313 " pdb=" CB LEU B 313 " pdb=" CD1 LEU B 313 " pdb=" CD2 LEU B 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 547 " pdb=" N ILE A 547 " pdb=" C ILE A 547 " pdb=" CB ILE A 547 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA LEU A 549 " pdb=" N LEU A 549 " pdb=" C LEU A 549 " pdb=" CB LEU A 549 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 2204 not shown) Planarity restraints: 2316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 324 " -0.035 2.00e-02 2.50e+03 2.76e-02 1.91e+01 pdb=" CG TRP D 324 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP D 324 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 324 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 324 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 324 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 324 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 324 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 324 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 324 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 238 " -0.055 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO C 239 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 239 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 239 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 449 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 450 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " 0.031 5.00e-02 4.00e+02 ... (remaining 2313 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 237 2.65 - 3.21: 12920 3.21 - 3.78: 22653 3.78 - 4.34: 29629 4.34 - 4.90: 47569 Nonbonded interactions: 113008 Sorted by model distance: nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.089 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.108 2.170 nonbonded pdb=" O3G AGS D 500 " pdb="MG MG E 401 " model vdw 2.111 2.170 nonbonded pdb=" O3G AGS C 401 " pdb="MG MG C 402 " model vdw 2.123 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.187 2.170 ... (remaining 113003 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.200 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 13959 Z= 0.185 Angle : 0.621 10.456 18994 Z= 0.316 Chirality : 0.041 0.206 2207 Planarity : 0.005 0.080 2316 Dihedral : 15.097 140.476 5404 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1637 helix: 0.92 (0.17), residues: 927 sheet: 0.00 (0.48), residues: 132 loop : -0.22 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP D 324 HIS 0.005 0.001 HIS D 340 PHE 0.018 0.001 PHE A 346 TYR 0.014 0.001 TYR E 92 ARG 0.007 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 232 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 LYS cc_start: 0.7309 (pptt) cc_final: 0.6821 (mmtt) REVERT: E 101 MET cc_start: 0.3852 (ppp) cc_final: 0.2888 (ppp) outliers start: 2 outliers final: 0 residues processed: 234 average time/residue: 0.2165 time to fit residues: 78.5032 Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 84 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 HIS B 26 ASN B 98 GLN B 108 HIS C 12 ASN C 105 GLN C 260 HIS E 93 HIS E 104 ASN E 110 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13959 Z= 0.215 Angle : 0.603 9.561 18994 Z= 0.311 Chirality : 0.041 0.142 2207 Planarity : 0.005 0.046 2316 Dihedral : 12.878 143.690 2136 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.51 % Allowed : 8.42 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1637 helix: 1.01 (0.17), residues: 962 sheet: -0.25 (0.49), residues: 127 loop : -0.14 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 324 HIS 0.008 0.001 HIS B 108 PHE 0.022 0.002 PHE A 443 TYR 0.017 0.001 TYR D 129 ARG 0.004 0.000 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 101 MET cc_start: 0.3904 (ppp) cc_final: 0.2994 (ppp) REVERT: E 229 ASN cc_start: 0.7872 (t0) cc_final: 0.7649 (t0) outliers start: 22 outliers final: 13 residues processed: 224 average time/residue: 0.2534 time to fit residues: 84.7681 Evaluate side-chains 196 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13959 Z= 0.267 Angle : 0.635 7.859 18994 Z= 0.325 Chirality : 0.042 0.169 2207 Planarity : 0.005 0.039 2316 Dihedral : 13.099 150.042 2136 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.71 % Allowed : 11.99 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1637 helix: 0.90 (0.17), residues: 979 sheet: -0.92 (0.46), residues: 140 loop : -0.19 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 327 HIS 0.015 0.001 HIS C 298 PHE 0.023 0.002 PHE D 290 TYR 0.016 0.001 TYR D 129 ARG 0.005 0.001 ARG D 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.4098 (mmp) cc_final: 0.3037 (mmm) REVERT: E 101 MET cc_start: 0.4239 (ppp) cc_final: 0.3265 (ppp) outliers start: 25 outliers final: 17 residues processed: 214 average time/residue: 0.2459 time to fit residues: 80.4725 Evaluate side-chains 195 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 178 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 255 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.0050 chunk 150 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 155 GLN C 12 ASN C 148 ASN C 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13959 Z= 0.297 Angle : 0.648 8.645 18994 Z= 0.333 Chirality : 0.043 0.279 2207 Planarity : 0.005 0.042 2316 Dihedral : 13.265 148.179 2136 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.67 % Allowed : 13.63 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1637 helix: 0.75 (0.16), residues: 988 sheet: -1.15 (0.47), residues: 127 loop : -0.27 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 256 HIS 0.010 0.001 HIS C 298 PHE 0.027 0.002 PHE D 203 TYR 0.017 0.002 TYR E 42 ARG 0.007 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.4534 (mtm) cc_final: 0.4317 (ptp) REVERT: B 290 LYS cc_start: 0.6779 (ptpp) cc_final: 0.6481 (ptmt) REVERT: C 22 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6738 (mt-10) REVERT: E 101 MET cc_start: 0.4296 (ppp) cc_final: 0.3274 (ppp) outliers start: 39 outliers final: 27 residues processed: 228 average time/residue: 0.2366 time to fit residues: 81.7096 Evaluate side-chains 201 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 98 GLN Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 307 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN B 210 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN D 288 ASN E 244 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13959 Z= 0.347 Angle : 0.704 8.570 18994 Z= 0.359 Chirality : 0.045 0.175 2207 Planarity : 0.005 0.049 2316 Dihedral : 13.594 151.436 2136 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.36 % Allowed : 15.68 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1637 helix: 0.49 (0.16), residues: 994 sheet: -1.36 (0.47), residues: 127 loop : -0.54 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 324 HIS 0.009 0.002 HIS C 298 PHE 0.028 0.002 PHE A 443 TYR 0.017 0.002 TYR D 129 ARG 0.008 0.001 ARG D 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 GLU cc_start: 0.6832 (tp30) cc_final: 0.5439 (tp30) REVERT: B 83 ASP cc_start: 0.5227 (m-30) cc_final: 0.3796 (p0) REVERT: B 290 LYS cc_start: 0.6865 (ptpp) cc_final: 0.6628 (ptmt) REVERT: C 22 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6920 (mt-10) REVERT: D 228 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6155 (tt) REVERT: E 101 MET cc_start: 0.4504 (ppp) cc_final: 0.3424 (ppp) REVERT: E 287 TYR cc_start: 0.7444 (m-80) cc_final: 0.6954 (m-80) outliers start: 49 outliers final: 32 residues processed: 227 average time/residue: 0.2520 time to fit residues: 84.7782 Evaluate side-chains 212 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 305 HIS Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 222 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 159 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.3483 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: