Starting phenix.real_space_refine on Tue Nov 18 07:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1p_8960/11_2025/6e1p_8960_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1p_8960/11_2025/6e1p_8960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e1p_8960/11_2025/6e1p_8960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1p_8960/11_2025/6e1p_8960.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1p_8960/11_2025/6e1p_8960_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1p_8960/11_2025/6e1p_8960_neut.cif" } resolution = 3.7 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= -0.000 sd= 1.000 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 1632 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 Ca 5 9.91 5 P 6 5.49 5 S 46 5.16 5 C 7154 2.51 5 N 1588 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5201 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'TPO:plan-1': 2, 'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5201 Classifications: {'peptide': 646} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 20, 'TRANS': 625} Chain breaks: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'TPO:plan-1': 2, 'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 100 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 146 Unusual residues: {' CA': 2, 'PLM': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 147 Unusual residues: {' CA': 3, 'PLM': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.25 Number of scatterers: 10697 At special positions: 0 Unit cell: (127.638, 91.17, 106.973, 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) Ca 5 19.99 S 46 16.00 P 6 15.00 O 1898 8.00 N 1588 7.00 C 7154 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 486.8 milliseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 77.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 35 through 46 removed outlier: 4.336A pdb=" N ASP A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 3.599A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 87 through 92 removed outlier: 3.726A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 removed outlier: 3.730A pdb=" N ILE A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 152 through 173 removed outlier: 3.759A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.624A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.912A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 238 removed outlier: 3.559A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.619A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.523A pdb=" N ILE A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.690A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.624A pdb=" N SER A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.702A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.714A pdb=" N GLU A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 349 through 354 removed outlier: 4.124A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.896A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.572A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 455 removed outlier: 4.120A pdb=" N LEU A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 removed outlier: 4.025A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 486 removed outlier: 4.302A pdb=" N ILE A 483 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 500 through 513 removed outlier: 3.591A pdb=" N TRP A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.675A pdb=" N TRP A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.792A pdb=" N LEU A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 550 removed outlier: 5.928A pdb=" N ARG A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 551 through 587 removed outlier: 3.750A pdb=" N ILE A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix removed outlier: 4.074A pdb=" N ILE A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 removed outlier: 3.854A pdb=" N PHE A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 601' Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.525A pdb=" N VAL A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 removed outlier: 3.869A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.077A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 693 removed outlier: 3.584A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 691 " --> pdb=" O CYS A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 46 removed outlier: 4.324A pdb=" N ASP B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.586A pdb=" N PHE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.506A pdb=" N LEU B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.930A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 removed outlier: 3.720A pdb=" N ILE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 152 through 173 removed outlier: 3.585A pdb=" N LYS B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.631A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.905A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.701A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.631A pdb=" N LEU B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.523A pdb=" N ILE B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.691A pdb=" N VAL B 270 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.581A pdb=" N SER B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.983A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 335 removed outlier: 3.719A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 349 through 355 removed outlier: 4.168A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 removed outlier: 3.568A pdb=" N PHE B 368 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 370 " --> pdb=" O GLU B 366 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 399 removed outlier: 3.563A pdb=" N ALA B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 455 removed outlier: 3.669A pdb=" N PHE B 438 " --> pdb=" O TYR B 434 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 448 " --> pdb=" O PHE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 removed outlier: 4.006A pdb=" N ALA B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.504A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 Processing helix chain 'B' and resid 500 through 513 removed outlier: 3.569A pdb=" N TRP B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 513 " --> pdb=" O ILE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 532 removed outlier: 3.800A pdb=" N ILE B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG B 531 " --> pdb=" O GLY B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.637A pdb=" N ARG B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 removed outlier: 6.088A pdb=" N ARG B 550 " --> pdb=" O ASN B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 551 through 587 removed outlier: 3.514A pdb=" N ALA B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 558 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Proline residue: B 567 - end of helix removed outlier: 4.068A pdb=" N ILE B 572 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 581 " --> pdb=" O CYS B 577 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 601 removed outlier: 3.904A pdb=" N PHE B 599 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 595 through 601' Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 615 through 629 removed outlier: 3.526A pdb=" N VAL B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.866A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.079A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 693 removed outlier: 3.624A pdb=" N LEU B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 680 " --> pdb=" O PHE B 676 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 682 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1509 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: 1.50 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3049 1.34 - 1.46: 2399 1.46 - 1.58: 5400 1.58 - 1.70: 20 1.70 - 1.82: 74 Bond restraints: 10942 Sorted by residual: bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.604 0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O1P TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 13970 2.43 - 4.86: 665 4.86 - 7.28: 121 7.28 - 9.71: 43 9.71 - 12.14: 9 Bond angle restraints: 14808 Sorted by residual: angle pdb=" N PHE B 611 " pdb=" CA PHE B 611 " pdb=" CB PHE B 611 " ideal model delta sigma weight residual 110.49 99.93 10.56 1.69e+00 3.50e-01 3.90e+01 angle pdb=" C LEU B 610 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.84e+01 angle pdb=" C SER A 150 " pdb=" N ARG A 151 " pdb=" CA ARG A 151 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N ASN B 612 " pdb=" CA ASN B 612 " pdb=" C ASN B 612 " ideal model delta sigma weight residual 110.80 121.78 -10.98 2.13e+00 2.20e-01 2.66e+01 angle pdb=" C ILE B 371 " pdb=" N PHE B 372 " pdb=" CA PHE B 372 " ideal model delta sigma weight residual 120.79 127.69 -6.90 1.39e+00 5.18e-01 2.46e+01 ... (remaining 14803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 5742 15.01 - 30.02: 425 30.02 - 45.03: 138 45.03 - 60.03: 75 60.03 - 75.04: 2 Dihedral angle restraints: 6382 sinusoidal: 2568 harmonic: 3814 Sorted by residual: dihedral pdb=" CA LEU B 610 " pdb=" C LEU B 610 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " ideal model delta harmonic sigma weight residual -180.00 -130.54 -49.46 0 5.00e+00 4.00e-02 9.79e+01 dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LEU A 661 " pdb=" CA LEU A 661 " ideal model delta harmonic sigma weight residual 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.27e+01 dihedral pdb=" CA PHE A 611 " pdb=" C PHE A 611 " pdb=" N ASN A 612 " pdb=" CA ASN A 612 " ideal model delta harmonic sigma weight residual -180.00 -137.64 -42.36 0 5.00e+00 4.00e-02 7.18e+01 ... (remaining 6379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1469 0.085 - 0.171: 176 0.171 - 0.256: 19 0.256 - 0.342: 2 0.342 - 0.427: 2 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" CB TPO A 29 " pdb=" CA TPO A 29 " pdb=" OG1 TPO A 29 " pdb=" CG2 TPO A 29 " both_signs ideal model delta sigma weight residual False 2.48 2.77 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1665 not shown) Planarity restraints: 1810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 613 " 0.027 2.00e-02 2.50e+03 2.10e-02 7.75e+00 pdb=" CG PHE A 613 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 613 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 613 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 613 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 613 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 613 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 89 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO B 90 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 613 " -0.023 2.00e-02 2.50e+03 1.85e-02 5.96e+00 pdb=" CG PHE B 613 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 613 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 613 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 613 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 613 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 613 " -0.005 2.00e-02 2.50e+03 ... (remaining 1807 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 7 2.24 - 2.90: 4238 2.90 - 3.57: 15470 3.57 - 4.23: 24922 4.23 - 4.90: 39996 Nonbonded interactions: 84633 Sorted by model distance: nonbonded pdb=" CC PLM A 809 " pdb=" CA PLM B 804 " model vdw 1.571 3.072 nonbonded pdb=" C3 PLM A 810 " pdb=" C5 PLM B 803 " model vdw 1.742 3.072 nonbonded pdb=" O2P TPO A 26 " pdb=" O1P TPO A 29 " model vdw 2.090 3.040 nonbonded pdb=" OE2 GLU B 450 " pdb=" NH2 ARG B 531 " model vdw 2.179 3.120 nonbonded pdb=" OH TYR B 114 " pdb=" OD2 ASP B 615 " model vdw 2.183 3.040 ... (remaining 84628 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 22 through 801 or resid 803 through 804 or resid 807 throu \ gh 810)) selection = (chain 'B' and (resid 22 through 801 or resid 803 through 804 or resid 807 throu \ gh 810)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.010 0.113 10951 Z= 0.458 Angle : 1.296 12.140 14808 Z= 0.696 Chirality : 0.059 0.427 1668 Planarity : 0.007 0.063 1810 Dihedral : 14.000 75.042 3918 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 0.18 % Allowed : 2.28 % Favored : 97.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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 are not related in a simple way. whole: -5.32 (0.16), residues: 1262 helix: -3.67 (0.10), residues: 826 sheet: None (None), residues: 0 loop : -2.82 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 540 TYR 0.029 0.004 TYR A 579 PHE 0.048 0.004 PHE A 613 TRP 0.025 0.003 TRP A 280 HIS 0.002 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00994 (10942) covalent geometry : angle 1.29634 (14808) hydrogen bonds : bond 0.30103 ( 503) hydrogen bonds : angle 10.14032 ( 1509) Misc. bond : bond 0.03447 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.8048 (t70) cc_final: 0.7767 (t70) REVERT: A 71 ASP cc_start: 0.9382 (t0) cc_final: 0.8974 (t0) REVERT: A 77 ASN cc_start: 0.9363 (m-40) cc_final: 0.9119 (m110) REVERT: A 89 GLN cc_start: 0.8843 (mt0) cc_final: 0.8426 (mt0) REVERT: A 117 ASN cc_start: 0.9336 (m-40) cc_final: 0.8841 (t0) REVERT: A 137 PHE cc_start: 0.9127 (t80) cc_final: 0.8480 (t80) REVERT: A 195 PHE cc_start: 0.8901 (t80) cc_final: 0.8549 (t80) REVERT: A 204 ASP cc_start: 0.8801 (m-30) cc_final: 0.8529 (m-30) REVERT: A 212 MET cc_start: 0.9066 (ttp) cc_final: 0.8229 (ttp) REVERT: A 307 SER cc_start: 0.9323 (m) cc_final: 0.9099 (t) REVERT: A 320 ASP cc_start: 0.9270 (m-30) cc_final: 0.9037 (m-30) REVERT: A 322 MET cc_start: 0.8509 (tmm) cc_final: 0.8038 (tmm) REVERT: A 326 MET cc_start: 0.9053 (mmm) cc_final: 0.8456 (mmp) REVERT: A 333 LEU cc_start: 0.8218 (tp) cc_final: 0.7952 (tt) REVERT: A 450 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 562 ILE cc_start: 0.8974 (mt) cc_final: 0.8561 (mt) REVERT: A 602 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7937 (mp0) REVERT: A 603 LEU cc_start: 0.8028 (mt) cc_final: 0.7788 (mt) REVERT: A 617 PRO cc_start: 0.8316 (Cg_endo) cc_final: 0.8113 (Cg_exo) REVERT: A 620 MET cc_start: 0.8744 (mmm) cc_final: 0.8536 (tpp) REVERT: A 632 TRP cc_start: 0.8810 (p-90) cc_final: 0.8400 (p-90) REVERT: A 637 GLU cc_start: 0.8132 (tp30) cc_final: 0.7313 (tp30) REVERT: A 641 ASP cc_start: 0.9028 (m-30) cc_final: 0.8591 (t0) REVERT: A 648 SER cc_start: 0.9020 (m) cc_final: 0.8521 (p) REVERT: A 673 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8639 (mm-30) REVERT: A 675 PHE cc_start: 0.8181 (t80) cc_final: 0.7851 (t80) REVERT: A 678 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7989 (mm-30) REVERT: B 27 HIS cc_start: 0.8270 (t70) cc_final: 0.7957 (t70) REVERT: B 71 ASP cc_start: 0.9372 (t0) cc_final: 0.8969 (t0) REVERT: B 77 ASN cc_start: 0.9384 (m-40) cc_final: 0.9144 (m110) REVERT: B 137 PHE cc_start: 0.9134 (t80) cc_final: 0.8509 (t80) REVERT: B 195 PHE cc_start: 0.8876 (t80) cc_final: 0.8586 (t80) REVERT: B 204 ASP cc_start: 0.8796 (m-30) cc_final: 0.8526 (m-30) REVERT: B 212 MET cc_start: 0.9053 (ttp) cc_final: 0.8246 (ttp) REVERT: B 232 TRP cc_start: 0.9084 (t60) cc_final: 0.8710 (t60) REVERT: B 307 SER cc_start: 0.9336 (m) cc_final: 0.9092 (t) REVERT: B 320 ASP cc_start: 0.9284 (m-30) cc_final: 0.9052 (m-30) REVERT: B 322 MET cc_start: 0.8503 (tmm) cc_final: 0.8028 (tmm) REVERT: B 326 MET cc_start: 0.9070 (mmm) cc_final: 0.8467 (mmp) REVERT: B 333 LEU cc_start: 0.8213 (tp) cc_final: 0.7916 (tt) REVERT: B 450 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 542 ILE cc_start: 0.8829 (mt) cc_final: 0.8605 (mt) REVERT: B 602 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7820 (mp0) REVERT: B 635 TRP cc_start: 0.9050 (m-90) cc_final: 0.8743 (m-90) REVERT: B 637 GLU cc_start: 0.8091 (tp30) cc_final: 0.7509 (tp30) REVERT: B 641 ASP cc_start: 0.9030 (m-30) cc_final: 0.8592 (t0) REVERT: B 648 SER cc_start: 0.9037 (m) cc_final: 0.8538 (p) REVERT: B 673 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8647 (mm-30) REVERT: B 675 PHE cc_start: 0.8187 (t80) cc_final: 0.7946 (t80) REVERT: B 681 LEU cc_start: 0.7767 (mt) cc_final: 0.7410 (mt) outliers start: 2 outliers final: 2 residues processed: 490 average time/residue: 0.0853 time to fit residues: 61.7656 Evaluate side-chains 348 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 346 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 440 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 89 GLN A 346 GLN A 549 GLN B 89 GLN B 443 ASN B 454 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.199452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.152904 restraints weight = 17559.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.157495 restraints weight = 8112.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.160335 restraints weight = 5000.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.161954 restraints weight = 3727.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.162685 restraints weight = 3170.245| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10951 Z= 0.153 Angle : 0.743 8.401 14808 Z= 0.378 Chirality : 0.043 0.199 1668 Planarity : 0.005 0.040 1810 Dihedral : 13.441 59.654 1628 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 2.74 % Allowed : 15.97 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 are not related in a simple way. whole: -2.93 (0.21), residues: 1262 helix: -1.77 (0.15), residues: 850 sheet: None (None), residues: 0 loop : -1.93 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 398 TYR 0.026 0.002 TYR B 532 PHE 0.020 0.002 PHE B 554 TRP 0.014 0.001 TRP B 232 HIS 0.002 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00319 (10942) covalent geometry : angle 0.74252 (14808) hydrogen bonds : bond 0.05304 ( 503) hydrogen bonds : angle 5.51586 ( 1509) Misc. bond : bond 0.00096 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 432 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9316 (t0) cc_final: 0.8389 (t0) REVERT: A 137 PHE cc_start: 0.8921 (t80) cc_final: 0.8363 (t80) REVERT: A 151 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7507 (pmt-80) REVERT: A 156 LYS cc_start: 0.9234 (ttmt) cc_final: 0.9000 (mtmt) REVERT: A 203 ARG cc_start: 0.9010 (ttp-110) cc_final: 0.8486 (mtm-85) REVERT: A 232 TRP cc_start: 0.8508 (t60) cc_final: 0.8182 (t60) REVERT: A 295 PHE cc_start: 0.8416 (m-10) cc_final: 0.7903 (m-10) REVERT: A 322 MET cc_start: 0.8470 (tmm) cc_final: 0.8143 (tmm) REVERT: A 324 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7557 (ttt180) REVERT: A 326 MET cc_start: 0.8877 (mmm) cc_final: 0.8466 (mmp) REVERT: A 387 GLU cc_start: 0.9438 (mp0) cc_final: 0.8851 (mm-30) REVERT: A 388 PHE cc_start: 0.8690 (t80) cc_final: 0.8478 (t80) REVERT: A 561 LEU cc_start: 0.8718 (tp) cc_final: 0.7860 (tp) REVERT: A 598 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8837 (tp) REVERT: A 602 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7903 (mp0) REVERT: A 637 GLU cc_start: 0.7780 (tp30) cc_final: 0.7243 (tp30) REVERT: A 641 ASP cc_start: 0.8629 (m-30) cc_final: 0.8268 (t0) REVERT: A 648 SER cc_start: 0.8242 (m) cc_final: 0.8027 (p) REVERT: A 673 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8285 (mm-30) REVERT: A 678 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 71 ASP cc_start: 0.9404 (t0) cc_final: 0.8843 (t0) REVERT: B 137 PHE cc_start: 0.8974 (t80) cc_final: 0.8596 (t80) REVERT: B 203 ARG cc_start: 0.9014 (ttp-110) cc_final: 0.8501 (mtm-85) REVERT: B 295 PHE cc_start: 0.8384 (m-10) cc_final: 0.7933 (m-10) REVERT: B 322 MET cc_start: 0.8471 (tmm) cc_final: 0.8140 (tmm) REVERT: B 324 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7606 (ttt180) REVERT: B 326 MET cc_start: 0.8885 (mmm) cc_final: 0.8473 (mmp) REVERT: B 387 GLU cc_start: 0.9414 (mp0) cc_final: 0.8829 (mp0) REVERT: B 388 PHE cc_start: 0.8693 (t80) cc_final: 0.8419 (t80) REVERT: B 561 LEU cc_start: 0.8811 (tp) cc_final: 0.7768 (tp) REVERT: B 579 TYR cc_start: 0.9029 (m-80) cc_final: 0.8802 (m-80) REVERT: B 581 SER cc_start: 0.9221 (m) cc_final: 0.8952 (p) REVERT: B 598 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 602 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7894 (mp0) REVERT: B 603 LEU cc_start: 0.8127 (mt) cc_final: 0.7651 (mp) REVERT: B 610 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8161 (mm) REVERT: B 637 GLU cc_start: 0.7800 (tp30) cc_final: 0.7219 (tp30) REVERT: B 641 ASP cc_start: 0.8594 (m-30) cc_final: 0.8228 (t0) REVERT: B 648 SER cc_start: 0.8310 (m) cc_final: 0.8071 (p) REVERT: B 673 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8250 (mm-30) outliers start: 30 outliers final: 14 residues processed: 448 average time/residue: 0.0933 time to fit residues: 60.8288 Evaluate side-chains 387 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 369 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 33 optimal weight: 0.0270 chunk 38 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN B 77 ASN B 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.202226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.157847 restraints weight = 17635.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.162505 restraints weight = 8073.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.165393 restraints weight = 4908.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.167096 restraints weight = 3618.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.168113 restraints weight = 3050.739| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10951 Z= 0.125 Angle : 0.684 9.130 14808 Z= 0.337 Chirality : 0.042 0.160 1668 Planarity : 0.004 0.037 1810 Dihedral : 11.725 59.884 1626 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 3.10 % Allowed : 20.80 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -2.17 (0.22), residues: 1262 helix: -1.10 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.90 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 493 TYR 0.021 0.002 TYR A 123 PHE 0.021 0.001 PHE B 554 TRP 0.013 0.001 TRP B 271 HIS 0.008 0.002 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00262 (10942) covalent geometry : angle 0.68368 (14808) hydrogen bonds : bond 0.04081 ( 503) hydrogen bonds : angle 5.03194 ( 1509) Misc. bond : bond 0.00129 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 421 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.7273 (t70) cc_final: 0.6948 (t-90) REVERT: A 71 ASP cc_start: 0.9247 (t0) cc_final: 0.8271 (t0) REVERT: A 124 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8911 (mp0) REVERT: A 137 PHE cc_start: 0.8910 (t80) cc_final: 0.8276 (t80) REVERT: A 151 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7883 (pmt-80) REVERT: A 203 ARG cc_start: 0.9055 (ttp-110) cc_final: 0.8490 (mtm-85) REVERT: A 205 THR cc_start: 0.9565 (m) cc_final: 0.9161 (t) REVERT: A 219 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 232 TRP cc_start: 0.8484 (t60) cc_final: 0.8101 (t60) REVERT: A 295 PHE cc_start: 0.8428 (m-10) cc_final: 0.8013 (m-10) REVERT: A 322 MET cc_start: 0.8477 (tmm) cc_final: 0.8118 (tmm) REVERT: A 326 MET cc_start: 0.8842 (mmm) cc_final: 0.8443 (mmp) REVERT: A 386 ASP cc_start: 0.8936 (p0) cc_final: 0.8695 (p0) REVERT: A 387 GLU cc_start: 0.9383 (mp0) cc_final: 0.9057 (mp0) REVERT: A 393 GLN cc_start: 0.9009 (tp40) cc_final: 0.8776 (mt0) REVERT: A 602 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7915 (mp0) REVERT: A 637 GLU cc_start: 0.7694 (tp30) cc_final: 0.7175 (tp30) REVERT: A 641 ASP cc_start: 0.8592 (m-30) cc_final: 0.8115 (t0) REVERT: A 673 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8337 (mm-30) REVERT: B 71 ASP cc_start: 0.9204 (t0) cc_final: 0.8486 (t0) REVERT: B 137 PHE cc_start: 0.8914 (t80) cc_final: 0.8514 (t80) REVERT: B 205 THR cc_start: 0.9565 (m) cc_final: 0.9159 (t) REVERT: B 322 MET cc_start: 0.8483 (tmm) cc_final: 0.8127 (tmm) REVERT: B 324 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7662 (ttt180) REVERT: B 326 MET cc_start: 0.8816 (mmm) cc_final: 0.8432 (mmp) REVERT: B 387 GLU cc_start: 0.9291 (mp0) cc_final: 0.8957 (mp0) REVERT: B 393 GLN cc_start: 0.9041 (tp40) cc_final: 0.8786 (mt0) REVERT: B 542 ILE cc_start: 0.8661 (mt) cc_final: 0.8346 (mt) REVERT: B 546 MET cc_start: 0.6042 (mtm) cc_final: 0.5615 (mtm) REVERT: B 561 LEU cc_start: 0.8630 (tp) cc_final: 0.7626 (tp) REVERT: B 602 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7847 (mp0) REVERT: B 637 GLU cc_start: 0.7718 (tp30) cc_final: 0.7108 (tp30) REVERT: B 641 ASP cc_start: 0.8602 (m-30) cc_final: 0.8198 (t0) REVERT: B 648 SER cc_start: 0.8186 (m) cc_final: 0.7933 (p) outliers start: 34 outliers final: 21 residues processed: 432 average time/residue: 0.0891 time to fit residues: 56.9513 Evaluate side-chains 387 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 364 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 551 TYR Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 87 optimal weight: 0.0970 chunk 127 optimal weight: 0.6980 chunk 74 optimal weight: 0.0970 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.202847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156372 restraints weight = 17847.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.161117 restraints weight = 8338.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.164039 restraints weight = 5116.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.165771 restraints weight = 3785.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.166581 restraints weight = 3186.648| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10951 Z= 0.122 Angle : 0.679 8.556 14808 Z= 0.330 Chirality : 0.041 0.153 1668 Planarity : 0.004 0.057 1810 Dihedral : 10.946 59.559 1626 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.80 % Rotamer: Outliers : 2.92 % Allowed : 22.99 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -1.53 (0.23), residues: 1262 helix: -0.59 (0.17), residues: 876 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 493 TYR 0.019 0.002 TYR A 305 PHE 0.019 0.001 PHE B 554 TRP 0.013 0.001 TRP B 271 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00261 (10942) covalent geometry : angle 0.67922 (14808) hydrogen bonds : bond 0.03671 ( 503) hydrogen bonds : angle 4.84449 ( 1509) Misc. bond : bond 0.00126 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 410 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9338 (t0) cc_final: 0.8373 (t0) REVERT: A 89 GLN cc_start: 0.8218 (mt0) cc_final: 0.8017 (mt0) REVERT: A 137 PHE cc_start: 0.8846 (t80) cc_final: 0.8265 (t80) REVERT: A 151 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7843 (pmt-80) REVERT: A 212 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8271 (ttm) REVERT: A 219 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8640 (tp) REVERT: A 295 PHE cc_start: 0.8348 (m-10) cc_final: 0.7910 (m-10) REVERT: A 305 TYR cc_start: 0.8834 (t80) cc_final: 0.8507 (t80) REVERT: A 322 MET cc_start: 0.8502 (tmm) cc_final: 0.8136 (tmm) REVERT: A 326 MET cc_start: 0.8832 (mmm) cc_final: 0.8420 (mmp) REVERT: A 602 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8013 (mp0) REVERT: A 637 GLU cc_start: 0.7696 (tp30) cc_final: 0.7248 (tp30) REVERT: A 641 ASP cc_start: 0.8592 (m-30) cc_final: 0.8151 (t0) REVERT: B 71 ASP cc_start: 0.9246 (t0) cc_final: 0.8692 (t0) REVERT: B 137 PHE cc_start: 0.8926 (t80) cc_final: 0.8451 (t80) REVERT: B 148 TRP cc_start: 0.8818 (m100) cc_final: 0.8509 (m-10) REVERT: B 205 THR cc_start: 0.9505 (m) cc_final: 0.9063 (t) REVERT: B 212 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: B 232 TRP cc_start: 0.8532 (t60) cc_final: 0.8209 (t60) REVERT: B 322 MET cc_start: 0.8504 (tmm) cc_final: 0.8154 (tmm) REVERT: B 324 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7615 (ttt180) REVERT: B 326 MET cc_start: 0.8828 (mmm) cc_final: 0.8439 (mmp) REVERT: B 387 GLU cc_start: 0.9336 (mp0) cc_final: 0.8948 (mp0) REVERT: B 393 GLN cc_start: 0.9052 (tp40) cc_final: 0.8803 (mt0) REVERT: B 542 ILE cc_start: 0.8678 (mt) cc_final: 0.8390 (mt) REVERT: B 561 LEU cc_start: 0.8668 (tp) cc_final: 0.7756 (tp) REVERT: B 602 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7868 (mp0) REVERT: B 637 GLU cc_start: 0.7598 (tp30) cc_final: 0.6973 (tp30) outliers start: 32 outliers final: 22 residues processed: 419 average time/residue: 0.0861 time to fit residues: 53.3647 Evaluate side-chains 406 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 380 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 15 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.202962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.156483 restraints weight = 17581.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.161121 restraints weight = 8259.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.163965 restraints weight = 5068.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.165405 restraints weight = 3763.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166512 restraints weight = 3223.917| |-----------------------------------------------------------------------------| r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10951 Z= 0.126 Angle : 0.694 10.221 14808 Z= 0.334 Chirality : 0.041 0.173 1668 Planarity : 0.004 0.055 1810 Dihedral : 10.445 59.917 1626 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 3.74 % Allowed : 23.72 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.95 (0.24), residues: 1262 helix: -0.17 (0.17), residues: 862 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 493 TYR 0.026 0.001 TYR B 656 PHE 0.018 0.001 PHE B 554 TRP 0.011 0.001 TRP B 271 HIS 0.001 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00280 (10942) covalent geometry : angle 0.69410 (14808) hydrogen bonds : bond 0.03441 ( 503) hydrogen bonds : angle 4.74789 ( 1509) Misc. bond : bond 0.00131 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 402 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9337 (t0) cc_final: 0.8148 (t0) REVERT: A 137 PHE cc_start: 0.8760 (t80) cc_final: 0.8114 (t80) REVERT: A 151 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7904 (pmt-80) REVERT: A 219 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8663 (tp) REVERT: A 322 MET cc_start: 0.8462 (tmm) cc_final: 0.8213 (tmm) REVERT: A 326 MET cc_start: 0.8776 (mmm) cc_final: 0.8389 (mmp) REVERT: A 393 GLN cc_start: 0.9017 (tp40) cc_final: 0.8750 (mt0) REVERT: A 450 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 637 GLU cc_start: 0.7614 (tp30) cc_final: 0.7167 (tp30) REVERT: A 641 ASP cc_start: 0.8523 (m-30) cc_final: 0.8126 (t0) REVERT: A 673 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8136 (mm-30) REVERT: A 675 PHE cc_start: 0.8641 (t80) cc_final: 0.8368 (t80) REVERT: A 679 LEU cc_start: 0.7762 (tt) cc_final: 0.7335 (tt) REVERT: B 71 ASP cc_start: 0.9253 (t0) cc_final: 0.8702 (t0) REVERT: B 137 PHE cc_start: 0.8826 (t80) cc_final: 0.8471 (t80) REVERT: B 148 TRP cc_start: 0.8802 (m100) cc_final: 0.8593 (m-10) REVERT: B 200 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7994 (ptt-90) REVERT: B 205 THR cc_start: 0.9489 (m) cc_final: 0.9043 (t) REVERT: B 212 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7979 (mtm) REVERT: B 219 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8701 (tp) REVERT: B 232 TRP cc_start: 0.8551 (t60) cc_final: 0.8217 (t60) REVERT: B 306 ASP cc_start: 0.8056 (t0) cc_final: 0.7804 (m-30) REVERT: B 322 MET cc_start: 0.8464 (tmm) cc_final: 0.8197 (tmm) REVERT: B 324 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7609 (ttt180) REVERT: B 326 MET cc_start: 0.8811 (mmm) cc_final: 0.8413 (mmp) REVERT: B 387 GLU cc_start: 0.9469 (mp0) cc_final: 0.8942 (mp0) REVERT: B 393 GLN cc_start: 0.8941 (tp40) cc_final: 0.8722 (mt0) REVERT: B 641 ASP cc_start: 0.8529 (m-30) cc_final: 0.8198 (t0) outliers start: 41 outliers final: 27 residues processed: 416 average time/residue: 0.0907 time to fit residues: 55.5057 Evaluate side-chains 402 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 371 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.202598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.154040 restraints weight = 18463.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.158869 restraints weight = 8514.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.161850 restraints weight = 5252.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.163567 restraints weight = 3902.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164484 restraints weight = 3303.277| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10951 Z= 0.132 Angle : 0.699 9.250 14808 Z= 0.338 Chirality : 0.041 0.167 1668 Planarity : 0.004 0.053 1810 Dihedral : 10.215 59.314 1624 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.12 % Favored : 95.80 % Rotamer: Outliers : 4.29 % Allowed : 24.27 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.89 (0.24), residues: 1262 helix: -0.09 (0.17), residues: 886 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.026 0.002 TYR B 656 PHE 0.021 0.001 PHE A 554 TRP 0.012 0.001 TRP B 271 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00295 (10942) covalent geometry : angle 0.69925 (14808) hydrogen bonds : bond 0.03391 ( 503) hydrogen bonds : angle 4.71778 ( 1509) Misc. bond : bond 0.00128 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 397 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.9366 (t0) cc_final: 0.8446 (t0) REVERT: A 137 PHE cc_start: 0.8854 (t80) cc_final: 0.8201 (t80) REVERT: A 149 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 151 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7871 (pmt-80) REVERT: A 219 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8630 (tp) REVERT: A 232 TRP cc_start: 0.8470 (t60) cc_final: 0.8267 (t60) REVERT: A 322 MET cc_start: 0.8515 (tmm) cc_final: 0.8181 (tmm) REVERT: A 324 ARG cc_start: 0.5273 (ttt180) cc_final: 0.4982 (ttt180) REVERT: A 326 MET cc_start: 0.8849 (mmm) cc_final: 0.8336 (mmp) REVERT: A 387 GLU cc_start: 0.9431 (mp0) cc_final: 0.9073 (mp0) REVERT: A 632 TRP cc_start: 0.8594 (p-90) cc_final: 0.8306 (p-90) REVERT: A 637 GLU cc_start: 0.7583 (tp30) cc_final: 0.7125 (tp30) REVERT: B 71 ASP cc_start: 0.9296 (t0) cc_final: 0.8722 (t0) REVERT: B 137 PHE cc_start: 0.8922 (t80) cc_final: 0.8411 (t80) REVERT: B 191 ARG cc_start: 0.9132 (ptp-170) cc_final: 0.8892 (ptm160) REVERT: B 212 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: B 232 TRP cc_start: 0.8594 (t60) cc_final: 0.8257 (t60) REVERT: B 245 LEU cc_start: 0.8995 (tt) cc_final: 0.8483 (mp) REVERT: B 322 MET cc_start: 0.8519 (tmm) cc_final: 0.8166 (tmm) REVERT: B 326 MET cc_start: 0.8901 (mmm) cc_final: 0.8443 (mmp) REVERT: B 375 LEU cc_start: 0.3803 (OUTLIER) cc_final: 0.3559 (pp) REVERT: B 386 ASP cc_start: 0.9044 (p0) cc_final: 0.8687 (p0) REVERT: B 387 GLU cc_start: 0.9473 (mp0) cc_final: 0.9117 (mm-30) REVERT: B 393 GLN cc_start: 0.9012 (tp40) cc_final: 0.8777 (mt0) REVERT: B 546 MET cc_start: 0.4283 (mmm) cc_final: 0.4057 (mmm) REVERT: B 598 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8781 (tt) REVERT: B 602 GLU cc_start: 0.7872 (tp30) cc_final: 0.7390 (tp30) REVERT: B 603 LEU cc_start: 0.8068 (mt) cc_final: 0.7715 (tp) REVERT: B 641 ASP cc_start: 0.8511 (m-30) cc_final: 0.8227 (t0) REVERT: B 679 LEU cc_start: 0.7861 (tt) cc_final: 0.7440 (tt) REVERT: B 684 GLU cc_start: 0.7894 (pp20) cc_final: 0.7171 (mm-30) outliers start: 47 outliers final: 32 residues processed: 416 average time/residue: 0.0908 time to fit residues: 55.5995 Evaluate side-chains 406 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 368 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 212 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN B 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.201931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.155138 restraints weight = 17729.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.159578 restraints weight = 8389.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.162358 restraints weight = 5188.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.163939 restraints weight = 3875.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.164876 restraints weight = 3293.963| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10951 Z= 0.133 Angle : 0.705 9.799 14808 Z= 0.340 Chirality : 0.042 0.168 1668 Planarity : 0.004 0.054 1810 Dihedral : 10.093 59.974 1624 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.29 % Allowed : 25.00 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.76 (0.24), residues: 1262 helix: -0.04 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.42 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 493 TYR 0.027 0.002 TYR A 656 PHE 0.025 0.001 PHE B 285 TRP 0.013 0.001 TRP B 271 HIS 0.001 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00298 (10942) covalent geometry : angle 0.70518 (14808) hydrogen bonds : bond 0.03313 ( 503) hydrogen bonds : angle 4.70413 ( 1509) Misc. bond : bond 0.00128 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 373 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: A 137 PHE cc_start: 0.8705 (t80) cc_final: 0.8446 (t80) REVERT: A 149 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8219 (p) REVERT: A 151 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7730 (pmt-80) REVERT: A 203 ARG cc_start: 0.8985 (ttp-110) cc_final: 0.8772 (ttp-110) REVERT: A 219 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8696 (tp) REVERT: A 225 LEU cc_start: 0.9083 (mp) cc_final: 0.8740 (mp) REVERT: A 285 PHE cc_start: 0.8851 (m-80) cc_final: 0.8567 (m-10) REVERT: A 322 MET cc_start: 0.8405 (tmm) cc_final: 0.8112 (tmm) REVERT: A 326 MET cc_start: 0.8784 (mmm) cc_final: 0.8284 (mmp) REVERT: A 375 LEU cc_start: 0.3696 (OUTLIER) cc_final: 0.3475 (pp) REVERT: A 387 GLU cc_start: 0.9384 (mp0) cc_final: 0.9046 (mp0) REVERT: A 632 TRP cc_start: 0.8565 (p-90) cc_final: 0.8303 (p-90) REVERT: A 637 GLU cc_start: 0.7618 (tp30) cc_final: 0.7293 (tp30) REVERT: A 679 LEU cc_start: 0.7992 (tt) cc_final: 0.7516 (tt) REVERT: B 71 ASP cc_start: 0.9262 (t0) cc_final: 0.8627 (t0) REVERT: B 137 PHE cc_start: 0.8845 (t80) cc_final: 0.8348 (t80) REVERT: B 191 ARG cc_start: 0.9086 (ptp-170) cc_final: 0.8714 (ptm160) REVERT: B 232 TRP cc_start: 0.8502 (t60) cc_final: 0.8164 (t60) REVERT: B 322 MET cc_start: 0.8500 (tmm) cc_final: 0.8211 (tmm) REVERT: B 326 MET cc_start: 0.8747 (mmm) cc_final: 0.8286 (mmp) REVERT: B 341 GLU cc_start: 0.7628 (tp30) cc_final: 0.6923 (tp30) REVERT: B 386 ASP cc_start: 0.8914 (p0) cc_final: 0.8528 (p0) REVERT: B 387 GLU cc_start: 0.9458 (mp0) cc_final: 0.9130 (mm-30) REVERT: B 535 LEU cc_start: 0.8652 (mp) cc_final: 0.8265 (mm) REVERT: B 546 MET cc_start: 0.4559 (mmm) cc_final: 0.4218 (mmm) REVERT: B 603 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8023 (tp) REVERT: B 641 ASP cc_start: 0.8482 (m-30) cc_final: 0.8227 (t0) REVERT: B 684 GLU cc_start: 0.7649 (pp20) cc_final: 0.6979 (tp30) outliers start: 47 outliers final: 33 residues processed: 393 average time/residue: 0.0876 time to fit residues: 51.0035 Evaluate side-chains 391 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 352 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 399 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 0.0670 chunk 59 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 73 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.204160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.157185 restraints weight = 17735.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.161821 restraints weight = 8368.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.164676 restraints weight = 5162.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.166341 restraints weight = 3836.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.167105 restraints weight = 3238.914| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10951 Z= 0.123 Angle : 0.718 10.175 14808 Z= 0.341 Chirality : 0.042 0.176 1668 Planarity : 0.004 0.049 1810 Dihedral : 9.702 59.434 1624 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.65 % Allowed : 26.46 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.70 (0.24), residues: 1262 helix: -0.01 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 493 TYR 0.027 0.001 TYR A 656 PHE 0.025 0.001 PHE B 171 TRP 0.011 0.001 TRP A 271 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00270 (10942) covalent geometry : angle 0.71836 (14808) hydrogen bonds : bond 0.03262 ( 503) hydrogen bonds : angle 4.66365 ( 1509) Misc. bond : bond 0.00129 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 373 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8121 (p0) REVERT: A 137 PHE cc_start: 0.8747 (t80) cc_final: 0.8442 (t80) REVERT: A 149 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 151 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7857 (pmt-80) REVERT: A 152 LEU cc_start: 0.9060 (mp) cc_final: 0.8799 (pt) REVERT: A 212 MET cc_start: 0.7535 (mmp) cc_final: 0.7099 (mmt) REVERT: A 219 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8662 (tp) REVERT: A 227 LEU cc_start: 0.9331 (tp) cc_final: 0.9058 (tp) REVERT: A 271 TRP cc_start: 0.8385 (p-90) cc_final: 0.8182 (p-90) REVERT: A 285 PHE cc_start: 0.8908 (m-80) cc_final: 0.8610 (m-10) REVERT: A 322 MET cc_start: 0.8496 (tmm) cc_final: 0.8208 (tmm) REVERT: A 326 MET cc_start: 0.8739 (mmm) cc_final: 0.8276 (mmp) REVERT: A 387 GLU cc_start: 0.9430 (mp0) cc_final: 0.9218 (mp0) REVERT: A 632 TRP cc_start: 0.8650 (p-90) cc_final: 0.8394 (p-90) REVERT: A 637 GLU cc_start: 0.7721 (tp30) cc_final: 0.7341 (tp30) REVERT: B 71 ASP cc_start: 0.9289 (t0) cc_final: 0.8605 (t0) REVERT: B 137 PHE cc_start: 0.8852 (t80) cc_final: 0.8355 (t80) REVERT: B 191 ARG cc_start: 0.9052 (ptp-170) cc_final: 0.8636 (ptm160) REVERT: B 232 TRP cc_start: 0.8531 (t60) cc_final: 0.8157 (t60) REVERT: B 322 MET cc_start: 0.8499 (tmm) cc_final: 0.8175 (tmm) REVERT: B 326 MET cc_start: 0.8773 (mmm) cc_final: 0.8302 (mmp) REVERT: B 341 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6790 (tp30) REVERT: B 386 ASP cc_start: 0.8829 (p0) cc_final: 0.8307 (p0) REVERT: B 387 GLU cc_start: 0.9453 (mp0) cc_final: 0.8867 (mp0) REVERT: B 546 MET cc_start: 0.5054 (mmm) cc_final: 0.4743 (mmm) REVERT: B 641 ASP cc_start: 0.8455 (m-30) cc_final: 0.8179 (t0) REVERT: B 684 GLU cc_start: 0.7481 (pp20) cc_final: 0.6792 (tp30) outliers start: 40 outliers final: 29 residues processed: 392 average time/residue: 0.0850 time to fit residues: 49.8288 Evaluate side-chains 397 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 363 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.201486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.153982 restraints weight = 17757.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.158514 restraints weight = 8359.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.161342 restraints weight = 5151.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.162941 restraints weight = 3831.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.163880 restraints weight = 3245.423| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10951 Z= 0.146 Angle : 0.733 9.910 14808 Z= 0.352 Chirality : 0.042 0.198 1668 Planarity : 0.004 0.044 1810 Dihedral : 9.825 59.613 1624 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 3.74 % Allowed : 26.92 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 are not related in a simple way. whole: -0.65 (0.24), residues: 1262 helix: 0.02 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.29 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 493 TYR 0.026 0.002 TYR A 656 PHE 0.024 0.001 PHE B 285 TRP 0.011 0.001 TRP A 232 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00331 (10942) covalent geometry : angle 0.73262 (14808) hydrogen bonds : bond 0.03393 ( 503) hydrogen bonds : angle 4.75817 ( 1509) Misc. bond : bond 0.00127 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 352 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 PHE cc_start: 0.8673 (t80) cc_final: 0.8384 (t80) REVERT: A 149 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 151 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7917 (pmt-80) REVERT: A 170 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7241 (t0) REVERT: A 189 TYR cc_start: 0.8293 (m-10) cc_final: 0.7215 (m-10) REVERT: A 219 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8687 (tp) REVERT: A 285 PHE cc_start: 0.8949 (m-80) cc_final: 0.8589 (m-10) REVERT: A 322 MET cc_start: 0.8440 (tmm) cc_final: 0.8126 (tmm) REVERT: A 326 MET cc_start: 0.8759 (mmm) cc_final: 0.8281 (mmp) REVERT: A 612 ASN cc_start: 0.8108 (t0) cc_final: 0.7434 (t0) REVERT: A 632 TRP cc_start: 0.8669 (p-90) cc_final: 0.8382 (p-90) REVERT: A 637 GLU cc_start: 0.7778 (tp30) cc_final: 0.7349 (tp30) REVERT: A 679 LEU cc_start: 0.7972 (tt) cc_final: 0.7484 (tt) REVERT: B 71 ASP cc_start: 0.9253 (t0) cc_final: 0.8528 (t0) REVERT: B 137 PHE cc_start: 0.8865 (t80) cc_final: 0.8332 (t80) REVERT: B 191 ARG cc_start: 0.9074 (ptp-170) cc_final: 0.8626 (ptm160) REVERT: B 212 MET cc_start: 0.8488 (tpp) cc_final: 0.8033 (mmt) REVERT: B 232 TRP cc_start: 0.8559 (t60) cc_final: 0.8201 (t60) REVERT: B 245 LEU cc_start: 0.8974 (tt) cc_final: 0.8267 (mp) REVERT: B 322 MET cc_start: 0.8480 (tmm) cc_final: 0.8140 (tmm) REVERT: B 326 MET cc_start: 0.8779 (mmm) cc_final: 0.8292 (mmp) REVERT: B 341 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6903 (tp30) REVERT: B 386 ASP cc_start: 0.8785 (p0) cc_final: 0.8231 (p0) REVERT: B 387 GLU cc_start: 0.9426 (mp0) cc_final: 0.8855 (mp0) REVERT: B 450 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 546 MET cc_start: 0.5149 (mmm) cc_final: 0.4802 (mmm) REVERT: B 602 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7478 (tp30) REVERT: B 679 LEU cc_start: 0.8081 (tt) cc_final: 0.7581 (tt) REVERT: B 684 GLU cc_start: 0.7401 (pp20) cc_final: 0.6717 (tp30) outliers start: 41 outliers final: 32 residues processed: 369 average time/residue: 0.0851 time to fit residues: 46.6338 Evaluate side-chains 371 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 333 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.204267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.156760 restraints weight = 17705.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.161332 restraints weight = 8366.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.164214 restraints weight = 5145.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.165913 restraints weight = 3820.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166883 restraints weight = 3208.516| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10951 Z= 0.126 Angle : 0.757 10.513 14808 Z= 0.359 Chirality : 0.042 0.209 1668 Planarity : 0.004 0.043 1810 Dihedral : 9.412 59.686 1624 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.19 % Allowed : 27.46 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.59 (0.24), residues: 1262 helix: 0.05 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.21 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 493 TYR 0.026 0.001 TYR A 656 PHE 0.022 0.001 PHE B 171 TRP 0.011 0.001 TRP A 232 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00278 (10942) covalent geometry : angle 0.75748 (14808) hydrogen bonds : bond 0.03310 ( 503) hydrogen bonds : angle 4.67838 ( 1509) Misc. bond : bond 0.00129 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 368 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8075 (p0) REVERT: A 121 ILE cc_start: 0.9537 (mm) cc_final: 0.9253 (mm) REVERT: A 137 PHE cc_start: 0.8697 (t80) cc_final: 0.8382 (t80) REVERT: A 149 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8145 (p) REVERT: A 151 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7907 (pmt-80) REVERT: A 189 TYR cc_start: 0.8237 (m-10) cc_final: 0.7159 (m-10) REVERT: A 225 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8744 (mp) REVERT: A 285 PHE cc_start: 0.8893 (m-80) cc_final: 0.8594 (m-10) REVERT: A 322 MET cc_start: 0.8427 (tmm) cc_final: 0.8120 (tmm) REVERT: A 326 MET cc_start: 0.8765 (mmm) cc_final: 0.8325 (mmp) REVERT: A 387 GLU cc_start: 0.9425 (mp0) cc_final: 0.9084 (mp0) REVERT: A 632 TRP cc_start: 0.8619 (p-90) cc_final: 0.8360 (p-90) REVERT: A 637 GLU cc_start: 0.7763 (tp30) cc_final: 0.7329 (tp30) REVERT: B 71 ASP cc_start: 0.9244 (t0) cc_final: 0.8415 (t0) REVERT: B 137 PHE cc_start: 0.8854 (t80) cc_final: 0.8341 (t80) REVERT: B 191 ARG cc_start: 0.9079 (ptp-170) cc_final: 0.8760 (ptm160) REVERT: B 232 TRP cc_start: 0.8509 (t60) cc_final: 0.8151 (t60) REVERT: B 322 MET cc_start: 0.8535 (tmm) cc_final: 0.8171 (tmm) REVERT: B 326 MET cc_start: 0.8814 (mmm) cc_final: 0.8340 (mmp) REVERT: B 341 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6791 (tp30) REVERT: B 386 ASP cc_start: 0.8802 (p0) cc_final: 0.8265 (p0) REVERT: B 387 GLU cc_start: 0.9434 (mp0) cc_final: 0.8851 (mp0) REVERT: B 546 MET cc_start: 0.5435 (mmm) cc_final: 0.5121 (mmm) REVERT: B 602 GLU cc_start: 0.7583 (tp30) cc_final: 0.7316 (tp30) REVERT: B 603 LEU cc_start: 0.8036 (tp) cc_final: 0.7692 (tp) REVERT: B 681 LEU cc_start: 0.8449 (mt) cc_final: 0.8234 (mt) REVERT: B 684 GLU cc_start: 0.7211 (pp20) cc_final: 0.6776 (tp30) outliers start: 35 outliers final: 27 residues processed: 384 average time/residue: 0.0849 time to fit residues: 48.4030 Evaluate side-chains 384 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 352 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 280 TRP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 122 optimal weight: 0.0370 chunk 2 optimal weight: 0.0010 chunk 118 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 102 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.205450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.158546 restraints weight = 17798.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.163233 restraints weight = 8353.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.166117 restraints weight = 5110.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167782 restraints weight = 3776.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.168730 restraints weight = 3180.218| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10951 Z= 0.126 Angle : 0.762 10.257 14808 Z= 0.362 Chirality : 0.042 0.284 1668 Planarity : 0.004 0.043 1810 Dihedral : 9.070 59.555 1624 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.19 % Allowed : 28.19 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1262 helix: 0.06 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -1.11 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 493 TYR 0.024 0.001 TYR A 656 PHE 0.021 0.001 PHE B 554 TRP 0.009 0.001 TRP A 271 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00277 (10942) covalent geometry : angle 0.76250 (14808) hydrogen bonds : bond 0.03335 ( 503) hydrogen bonds : angle 4.63603 ( 1509) Misc. bond : bond 0.00127 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.77 seconds wall clock time: 38 minutes 35.35 seconds (2315.35 seconds total)