Starting phenix.real_space_refine on Wed Mar 4 08:01:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppr_20446/03_2026/6ppr_20446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppr_20446/03_2026/6ppr_20446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ppr_20446/03_2026/6ppr_20446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppr_20446/03_2026/6ppr_20446.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppr_20446/03_2026/6ppr_20446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppr_20446/03_2026/6ppr_20446_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 35 5.49 5 S 40 5.16 5 C 7483 2.51 5 N 2210 2.21 5 O 2223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11995 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5558 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 44, 'TRANS': 715} Chain breaks: 14 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 14, 'GLN:plan1': 2, 'ARG:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 178 Chain: "A" Number of atoms: 5746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 5746 Classifications: {'peptide': 834} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 47, 'TRANS': 786} Chain breaks: 22 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 559 Unresolved non-hydrogen angles: 701 Unresolved non-hydrogen dihedrals: 430 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ASP:plan': 25, 'GLN:plan1': 10, 'ARG:plan': 25, 'GLU:plan': 34, 'ASN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 417 Chain: "X" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.38, per 1000 atoms: 0.20 Number of scatterers: 11995 At special positions: 0 Unit cell: (142.976, 93.0204, 105.079, 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) Fe 4 26.01 S 40 16.00 P 35 15.00 O 2223 8.00 N 2210 7.00 C 7483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 520.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE3 SF4 A1102 " - pdb=" SG CYS A1027 " Number of angles added : 12 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 45.0% alpha, 5.7% beta 3 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.534A pdb=" N ASN B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 removed outlier: 4.230A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.751A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.876A pdb=" N LEU B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 removed outlier: 3.866A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.614A pdb=" N THR B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 229 " --> pdb=" O MET B 225 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 removed outlier: 3.853A pdb=" N ALA B 241 " --> pdb=" O PRO B 237 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 244 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 4.131A pdb=" N MET B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 333 through 337 removed outlier: 4.067A pdb=" N PHE B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 337 " --> pdb=" O PRO B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 337' Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.871A pdb=" N ALA B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 369 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 417 removed outlier: 4.075A pdb=" N ASP B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 removed outlier: 3.562A pdb=" N ALA B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 474 removed outlier: 3.621A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 3.818A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 507 through 514 removed outlier: 3.511A pdb=" N GLU B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.839A pdb=" N VAL B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 528' Processing helix chain 'B' and resid 554 through 572 removed outlier: 3.945A pdb=" N GLU B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 563 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 590 removed outlier: 3.550A pdb=" N VAL B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 609 through 623 removed outlier: 3.506A pdb=" N ASP B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 618 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.703A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 759 removed outlier: 3.502A pdb=" N SER B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP B 733 " --> pdb=" O LYS B 729 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP B 743 " --> pdb=" O LYS B 739 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 750 " --> pdb=" O ARG B 746 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 756 " --> pdb=" O ARG B 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 removed outlier: 4.274A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 851 removed outlier: 3.810A pdb=" N GLN B 845 " --> pdb=" O HIS B 841 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 847 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 851 " --> pdb=" O VAL B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 876 removed outlier: 3.834A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.541A pdb=" N ASP A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.986A pdb=" N ALA A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.672A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 120 through 133 removed outlier: 3.979A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.979A pdb=" N THR A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.545A pdb=" N MET A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.680A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.718A pdb=" N ALA A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 202 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.668A pdb=" N GLU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.744A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.882A pdb=" N VAL A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 269' Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 316 through 327 removed outlier: 3.570A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.800A pdb=" N ILE A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.611A pdb=" N THR A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 402' Processing helix chain 'A' and resid 422 through 433 removed outlier: 3.759A pdb=" N LEU A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 447 removed outlier: 3.748A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.795A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 removed outlier: 3.592A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 505 removed outlier: 4.145A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.547A pdb=" N TRP A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 546 through 567 removed outlier: 3.623A pdb=" N GLN A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 584 removed outlier: 3.554A pdb=" N VAL A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 648 removed outlier: 3.630A pdb=" N LEU A 644 " --> pdb=" O GLY A 640 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP A 646 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 removed outlier: 3.848A pdb=" N ARG A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 4.186A pdb=" N ALA A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 removed outlier: 4.018A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 3.680A pdb=" N ALA A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 757 " --> pdb=" O CYS A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 801 removed outlier: 3.911A pdb=" N LEU A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 removed outlier: 3.562A pdb=" N ARG A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 830 removed outlier: 3.943A pdb=" N THR A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 829 " --> pdb=" O ARG A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 837 removed outlier: 3.522A pdb=" N SER A 837 " --> pdb=" O HIS A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 852 removed outlier: 3.542A pdb=" N LEU A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'A' and resid 863 through 884 removed outlier: 3.721A pdb=" N ASN A 867 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.918A pdb=" N LEU A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1012 removed outlier: 4.218A pdb=" N THR A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1015 No H-bonds generated for 'chain 'A' and resid 1013 through 1015' Processing helix chain 'A' and resid 1026 through 1030 removed outlier: 3.780A pdb=" N CYS A1030 " --> pdb=" O CYS A1027 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.257A pdb=" N VAL B 74 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER B 117 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY B 76 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 75 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 282 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL B 315 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 284 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N LEU B 351 " --> pdb=" O PRO B 41 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 43 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.730A pdb=" N ARG B 141 " --> pdb=" O MET B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 396 through 397 removed outlier: 5.729A pdb=" N ARG B 396 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 675 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA B 432 " --> pdb=" O ALA B 676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 353 removed outlier: 3.596A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 619 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA A 383 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA A 622 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 385 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 384 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 794 through 796 removed outlier: 6.717A pdb=" N ARG A 921 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR A 895 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLU A 923 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL A 893 " --> pdb=" O GLU A 923 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AA8, first strand: chain 'A' and resid 974 through 978 removed outlier: 3.894A pdb=" N THR A 988 " --> pdb=" O TYR A 978 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 6 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4966 1.42 - 1.64: 7232 1.64 - 1.85: 58 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12268 Sorted by residual: bond pdb=" N3B ANP A1101 " pdb=" PG ANP A1101 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP A1101 " pdb=" PB ANP A1101 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ARG B 385 " pdb=" CA ARG B 385 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N VAL A 904 " pdb=" CA VAL A 904 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.18e-02 7.18e+03 9.71e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15768 2.06 - 4.12: 937 4.12 - 6.19: 131 6.19 - 8.25: 52 8.25 - 10.31: 23 Bond angle restraints: 16911 Sorted by residual: angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" CB PRO B 208 " ideal model delta sigma weight residual 103.25 111.33 -8.08 1.05e+00 9.07e-01 5.92e+01 angle pdb=" N PRO B 211 " pdb=" CA PRO B 211 " pdb=" CB PRO B 211 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" N VAL B 756 " pdb=" CA VAL B 756 " pdb=" C VAL B 756 " ideal model delta sigma weight residual 112.29 107.04 5.25 9.40e-01 1.13e+00 3.12e+01 angle pdb=" C4' DC X 5 " pdb=" C3' DC X 5 " pdb=" O3' DC X 5 " ideal model delta sigma weight residual 110.00 117.53 -7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C4' DG X 12 " pdb=" C3' DG X 12 " pdb=" O3' DG X 12 " ideal model delta sigma weight residual 110.00 117.06 -7.06 1.50e+00 4.44e-01 2.22e+01 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 7022 35.43 - 70.87: 156 70.87 - 106.30: 11 106.30 - 141.73: 0 141.73 - 177.17: 6 Dihedral angle restraints: 7195 sinusoidal: 2669 harmonic: 4526 Sorted by residual: dihedral pdb=" CA LEU B 134 " pdb=" C LEU B 134 " pdb=" N PRO B 135 " pdb=" CA PRO B 135 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TYR A 859 " pdb=" C TYR A 859 " pdb=" N ASP A 860 " pdb=" CA ASP A 860 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLU A 814 " pdb=" C GLU A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 7192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1831 0.099 - 0.198: 214 0.198 - 0.297: 13 0.297 - 0.396: 1 0.396 - 0.495: 1 Chirality restraints: 2060 Sorted by residual: chirality pdb=" C3' DC X 5 " pdb=" C4' DC X 5 " pdb=" O3' DC X 5 " pdb=" C2' DC X 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C3' DG X 12 " pdb=" C4' DG X 12 " pdb=" O3' DG X 12 " pdb=" C2' DG X 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' ANP A1101 " pdb=" C2' ANP A1101 " pdb=" C4' ANP A1101 " pdb=" O3' ANP A1101 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2057 not shown) Planarity restraints: 2053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 261 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA B 261 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 261 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 348 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO B 349 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 807 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 808 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 808 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 808 " -0.041 5.00e-02 4.00e+02 ... (remaining 2050 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 86 2.61 - 3.18: 9331 3.18 - 3.75: 17014 3.75 - 4.33: 23114 4.33 - 4.90: 37601 Nonbonded interactions: 87146 Sorted by model distance: nonbonded pdb=" N2 DG X 12 " pdb=" O2 DC X 43 " model vdw 2.032 2.496 nonbonded pdb=" N GLU B 642 " pdb=" OE1 GLU B 642 " model vdw 2.078 3.120 nonbonded pdb=" CG2 VAL B 641 " pdb=" OE1 GLU B 642 " model vdw 2.113 3.460 nonbonded pdb=" CD1 LEU A 27 " pdb=" CA ALA A 281 " model vdw 2.202 3.890 nonbonded pdb=" OH TYR A 956 " pdb=" OP1 DT X 1 " model vdw 2.257 3.040 ... (remaining 87141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.040 Find NCS groups from input model: 0.090 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.017 0.817 12272 Z= 0.590 Angle : 1.422 53.073 16923 Z= 0.652 Chirality : 0.063 0.495 2060 Planarity : 0.008 0.076 2053 Dihedral : 15.432 177.166 4243 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.14 % Favored : 89.79 % Rotamer: Outliers : 1.28 % Allowed : 6.10 % Favored : 92.62 % 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: -6.00 (0.15), residues: 1518 helix: -4.70 (0.09), residues: 773 sheet: -2.49 (0.44), residues: 118 loop : -3.05 (0.20), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 232 TYR 0.027 0.003 TYR B 342 PHE 0.022 0.003 PHE A 618 TRP 0.039 0.004 TRP B 864 HIS 0.014 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00865 (12268) covalent geometry : angle 1.16157 (16911) hydrogen bonds : bond 0.34558 ( 310) hydrogen bonds : angle 10.38654 ( 890) metal coordination : bond 0.78285 ( 4) metal coordination : angle 30.85514 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: B 91 VAL cc_start: 0.8676 (t) cc_final: 0.8370 (m) REVERT: B 189 ASP cc_start: 0.7094 (t70) cc_final: 0.6828 (t0) REVERT: B 744 GLN cc_start: 0.8377 (tp-100) cc_final: 0.8155 (tp-100) REVERT: A 342 ASN cc_start: 0.8635 (t160) cc_final: 0.8365 (t0) outliers start: 13 outliers final: 3 residues processed: 248 average time/residue: 0.1564 time to fit residues: 50.4930 Evaluate side-chains 120 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 605 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 205 HIS B 229 GLN B 738 HIS ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN A 631 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121118 restraints weight = 17801.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121747 restraints weight = 14570.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122849 restraints weight = 12619.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123097 restraints weight = 9317.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123437 restraints weight = 8677.574| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12272 Z= 0.133 Angle : 0.778 23.409 16923 Z= 0.352 Chirality : 0.043 0.260 2060 Planarity : 0.006 0.049 2053 Dihedral : 17.034 176.933 2060 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.35 % Allowed : 11.52 % Favored : 85.14 % 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: -4.88 (0.18), residues: 1518 helix: -3.70 (0.12), residues: 790 sheet: -2.06 (0.46), residues: 118 loop : -2.56 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 921 TYR 0.016 0.002 TYR A 956 PHE 0.010 0.001 PHE B 622 TRP 0.016 0.002 TRP B 497 HIS 0.007 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00292 (12268) covalent geometry : angle 0.68253 (16911) hydrogen bonds : bond 0.05621 ( 310) hydrogen bonds : angle 5.35268 ( 890) metal coordination : bond 0.00982 ( 4) metal coordination : angle 14.05735 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.401 Fit side-chains REVERT: B 189 ASP cc_start: 0.7172 (t70) cc_final: 0.6873 (t0) REVERT: B 744 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7812 (tp-100) outliers start: 34 outliers final: 15 residues processed: 174 average time/residue: 0.1064 time to fit residues: 26.7731 Evaluate side-chains 125 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 342 ASN A 643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116625 restraints weight = 18123.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118345 restraints weight = 15825.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119104 restraints weight = 14926.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.118926 restraints weight = 9771.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119045 restraints weight = 10330.986| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12272 Z= 0.235 Angle : 0.837 27.472 16923 Z= 0.379 Chirality : 0.047 0.217 2060 Planarity : 0.005 0.048 2053 Dihedral : 16.776 178.121 2060 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.63 % Allowed : 12.80 % Favored : 82.58 % 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: -4.26 (0.19), residues: 1518 helix: -3.06 (0.15), residues: 797 sheet: -1.79 (0.50), residues: 114 loop : -2.46 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 871 TYR 0.021 0.002 TYR A 864 PHE 0.021 0.002 PHE B 340 TRP 0.016 0.002 TRP B 606 HIS 0.009 0.002 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00566 (12268) covalent geometry : angle 0.75100 (16911) hydrogen bonds : bond 0.05396 ( 310) hydrogen bonds : angle 4.97980 ( 890) metal coordination : bond 0.01174 ( 4) metal coordination : angle 13.89818 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: B 148 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 189 ASP cc_start: 0.7459 (t70) cc_final: 0.7088 (t0) REVERT: B 478 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8848 (tt) REVERT: A 27 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8546 (pp) outliers start: 47 outliers final: 23 residues processed: 155 average time/residue: 0.0846 time to fit residues: 20.2937 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 157 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122679 restraints weight = 17854.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124637 restraints weight = 15398.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125109 restraints weight = 11988.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124904 restraints weight = 9397.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124963 restraints weight = 9790.338| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12272 Z= 0.107 Angle : 0.675 23.488 16923 Z= 0.308 Chirality : 0.040 0.176 2060 Planarity : 0.004 0.044 2053 Dihedral : 16.439 179.184 2060 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.05 % Allowed : 14.57 % Favored : 82.38 % 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: -3.55 (0.20), residues: 1518 helix: -2.40 (0.16), residues: 797 sheet: -1.48 (0.51), residues: 115 loop : -2.24 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 178 TYR 0.012 0.001 TYR A 956 PHE 0.010 0.001 PHE A 879 TRP 0.012 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00237 (12268) covalent geometry : angle 0.59763 (16911) hydrogen bonds : bond 0.04073 ( 310) hydrogen bonds : angle 4.11802 ( 890) metal coordination : bond 0.00540 ( 4) metal coordination : angle 11.82580 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7221 (t70) cc_final: 0.6821 (t0) REVERT: A 27 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8380 (pp) REVERT: A 430 ASP cc_start: 0.7924 (t0) cc_final: 0.7557 (t0) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 0.0934 time to fit residues: 22.0040 Evaluate side-chains 127 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 142 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 304 HIS A 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121467 restraints weight = 17695.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123978 restraints weight = 15944.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124244 restraints weight = 13421.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123979 restraints weight = 9608.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124244 restraints weight = 10409.353| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12272 Z= 0.146 Angle : 0.711 23.823 16923 Z= 0.321 Chirality : 0.043 0.219 2060 Planarity : 0.004 0.064 2053 Dihedral : 16.343 177.680 2060 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.04 % Allowed : 15.85 % Favored : 80.12 % 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: -3.16 (0.21), residues: 1518 helix: -2.02 (0.17), residues: 796 sheet: -1.42 (0.51), residues: 118 loop : -2.14 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 871 TYR 0.014 0.002 TYR A 864 PHE 0.015 0.001 PHE B 340 TRP 0.017 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00346 (12268) covalent geometry : angle 0.63252 (16911) hydrogen bonds : bond 0.04244 ( 310) hydrogen bonds : angle 4.13279 ( 890) metal coordination : bond 0.00782 ( 4) metal coordination : angle 12.19337 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7322 (t70) cc_final: 0.6864 (t0) REVERT: A 27 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8414 (pp) REVERT: A 430 ASP cc_start: 0.7922 (t0) cc_final: 0.7563 (t0) outliers start: 41 outliers final: 27 residues processed: 144 average time/residue: 0.0855 time to fit residues: 18.9642 Evaluate side-chains 130 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 8 optimal weight: 0.0370 chunk 70 optimal weight: 0.5980 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123765 restraints weight = 17637.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.123409 restraints weight = 14725.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124631 restraints weight = 15696.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125116 restraints weight = 10494.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125289 restraints weight = 9766.938| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12272 Z= 0.120 Angle : 0.673 22.926 16923 Z= 0.304 Chirality : 0.041 0.199 2060 Planarity : 0.004 0.052 2053 Dihedral : 16.206 177.485 2060 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.64 % Allowed : 17.52 % Favored : 78.84 % 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: -2.82 (0.21), residues: 1518 helix: -1.67 (0.18), residues: 793 sheet: -1.29 (0.51), residues: 117 loop : -2.08 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 871 TYR 0.011 0.001 TYR A 864 PHE 0.011 0.001 PHE B 340 TRP 0.016 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00280 (12268) covalent geometry : angle 0.59966 (16911) hydrogen bonds : bond 0.03939 ( 310) hydrogen bonds : angle 3.91382 ( 890) metal coordination : bond 0.00625 ( 4) metal coordination : angle 11.49997 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7355 (t70) cc_final: 0.6915 (t0) REVERT: A 430 ASP cc_start: 0.7894 (t0) cc_final: 0.7579 (t0) REVERT: A 525 TRP cc_start: 0.7036 (t60) cc_final: 0.6612 (t-100) outliers start: 37 outliers final: 27 residues processed: 139 average time/residue: 0.0855 time to fit residues: 18.3832 Evaluate side-chains 128 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118402 restraints weight = 17680.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118977 restraints weight = 16064.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119891 restraints weight = 15843.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120408 restraints weight = 10436.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120374 restraints weight = 10513.396| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12272 Z= 0.180 Angle : 0.743 25.540 16923 Z= 0.335 Chirality : 0.044 0.232 2060 Planarity : 0.004 0.050 2053 Dihedral : 16.194 177.832 2058 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 4.33 % Allowed : 16.73 % Favored : 78.94 % 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: -2.72 (0.21), residues: 1518 helix: -1.57 (0.18), residues: 799 sheet: -1.40 (0.50), residues: 118 loop : -2.03 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 587 TYR 0.016 0.002 TYR A 864 PHE 0.018 0.002 PHE B 340 TRP 0.018 0.001 TRP A 787 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00430 (12268) covalent geometry : angle 0.66619 (16911) hydrogen bonds : bond 0.04298 ( 310) hydrogen bonds : angle 4.14244 ( 890) metal coordination : bond 0.01048 ( 4) metal coordination : angle 12.39769 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.6728 (t80) cc_final: 0.6414 (t80) REVERT: A 430 ASP cc_start: 0.7880 (t0) cc_final: 0.7531 (t0) outliers start: 44 outliers final: 34 residues processed: 144 average time/residue: 0.0897 time to fit residues: 19.8011 Evaluate side-chains 135 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 144 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 102 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123372 restraints weight = 17529.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125862 restraints weight = 15470.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126348 restraints weight = 12359.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126206 restraints weight = 8802.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126497 restraints weight = 8580.271| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12272 Z= 0.103 Angle : 0.657 21.975 16923 Z= 0.298 Chirality : 0.040 0.202 2060 Planarity : 0.004 0.043 2053 Dihedral : 15.902 177.706 2058 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.84 % Allowed : 17.32 % Favored : 78.84 % 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: -2.32 (0.22), residues: 1518 helix: -1.15 (0.19), residues: 792 sheet: -1.25 (0.51), residues: 119 loop : -1.97 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 751 TYR 0.008 0.001 TYR A 859 PHE 0.009 0.001 PHE A 879 TRP 0.016 0.001 TRP A 787 HIS 0.004 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00231 (12268) covalent geometry : angle 0.58844 (16911) hydrogen bonds : bond 0.03747 ( 310) hydrogen bonds : angle 3.72090 ( 890) metal coordination : bond 0.00484 ( 4) metal coordination : angle 11.01173 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.6766 (t80) cc_final: 0.6493 (t80) REVERT: A 430 ASP cc_start: 0.7877 (t0) cc_final: 0.7578 (t0) REVERT: A 525 TRP cc_start: 0.7080 (t60) cc_final: 0.6777 (t-100) outliers start: 39 outliers final: 24 residues processed: 151 average time/residue: 0.0821 time to fit residues: 19.3070 Evaluate side-chains 132 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 0.0770 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121033 restraints weight = 17528.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121390 restraints weight = 16240.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.122390 restraints weight = 15474.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122479 restraints weight = 11047.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122640 restraints weight = 10897.957| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12272 Z= 0.140 Angle : 0.698 23.255 16923 Z= 0.314 Chirality : 0.042 0.197 2060 Planarity : 0.004 0.045 2053 Dihedral : 15.830 177.495 2058 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.35 % Allowed : 18.21 % Favored : 78.44 % 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: -2.22 (0.22), residues: 1518 helix: -1.05 (0.19), residues: 798 sheet: -1.20 (0.51), residues: 117 loop : -1.97 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 587 TYR 0.013 0.001 TYR A 864 PHE 0.014 0.001 PHE B 340 TRP 0.015 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00335 (12268) covalent geometry : angle 0.62480 (16911) hydrogen bonds : bond 0.03924 ( 310) hydrogen bonds : angle 3.85769 ( 890) metal coordination : bond 0.00794 ( 4) metal coordination : angle 11.74403 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.6802 (t80) cc_final: 0.6515 (t80) REVERT: A 430 ASP cc_start: 0.7891 (t0) cc_final: 0.7596 (t0) REVERT: A 525 TRP cc_start: 0.7084 (t60) cc_final: 0.6785 (t-100) REVERT: A 801 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8817 (tm) outliers start: 34 outliers final: 29 residues processed: 136 average time/residue: 0.0860 time to fit residues: 18.1597 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 69 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.121689 restraints weight = 17727.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122606 restraints weight = 15838.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123518 restraints weight = 15066.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123775 restraints weight = 10953.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.124129 restraints weight = 10420.038| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12272 Z= 0.126 Angle : 0.691 23.085 16923 Z= 0.310 Chirality : 0.042 0.214 2060 Planarity : 0.004 0.042 2053 Dihedral : 15.789 177.468 2058 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.35 % Allowed : 18.31 % Favored : 78.35 % 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: -2.08 (0.22), residues: 1518 helix: -0.92 (0.19), residues: 799 sheet: -1.27 (0.51), residues: 119 loop : -1.90 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 587 TYR 0.011 0.001 TYR A 864 PHE 0.012 0.001 PHE B 340 TRP 0.015 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00297 (12268) covalent geometry : angle 0.61849 (16911) hydrogen bonds : bond 0.03867 ( 310) hydrogen bonds : angle 3.80692 ( 890) metal coordination : bond 0.00640 ( 4) metal coordination : angle 11.57378 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 313 TYR cc_start: 0.6810 (t80) cc_final: 0.6514 (t80) REVERT: A 430 ASP cc_start: 0.7875 (t0) cc_final: 0.7541 (t0) REVERT: A 525 TRP cc_start: 0.7069 (t60) cc_final: 0.6769 (t-100) REVERT: A 801 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8821 (tm) outliers start: 34 outliers final: 29 residues processed: 136 average time/residue: 0.0862 time to fit residues: 18.3014 Evaluate side-chains 138 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 142 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.0010 chunk 156 optimal weight: 2.9990 overall best weight: 0.6766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123833 restraints weight = 17448.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124780 restraints weight = 14371.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125950 restraints weight = 13764.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126095 restraints weight = 9546.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126236 restraints weight = 9030.086| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12272 Z= 0.107 Angle : 0.660 21.746 16923 Z= 0.298 Chirality : 0.041 0.221 2060 Planarity : 0.004 0.041 2053 Dihedral : 15.679 177.214 2058 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.25 % Allowed : 18.41 % Favored : 78.35 % 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: -1.82 (0.22), residues: 1518 helix: -0.68 (0.19), residues: 798 sheet: -1.21 (0.51), residues: 119 loop : -1.80 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 587 TYR 0.009 0.001 TYR A 859 PHE 0.009 0.001 PHE B 68 TRP 0.020 0.001 TRP A 149 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00246 (12268) covalent geometry : angle 0.59113 (16911) hydrogen bonds : bond 0.03659 ( 310) hydrogen bonds : angle 3.62927 ( 890) metal coordination : bond 0.00507 ( 4) metal coordination : angle 11.02619 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.75 seconds wall clock time: 28 minutes 57.84 seconds (1737.84 seconds total)