Starting phenix.real_space_refine on Fri Sep 11 22:32:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppr_20446/09_2026/6ppr_20446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppr_20446/09_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_20446/09_2026/6ppr_20446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppr_20446/09_2026/6ppr_20446.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppr_20446/09_2026/6ppr_20446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppr_20446/09_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-2.2.1-6174/lib/python3.11/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: 2.74, per 1000 atoms: 0.23 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: 1.08 Conformation dependent library (CDL) restraints added in 572.3 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: 1.11 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: 1.77 Time building geometry restraints manager: 1.40 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=" C3' DG X 56 " pdb=" O3' DG X 56 " ideal model delta sigma weight residual 1.435 1.480 -0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C3' DT X 57 " pdb=" O3' DT X 57 " ideal model delta sigma weight residual 1.435 1.392 0.043 1.30e-02 5.92e+03 1.12e+01 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15738 2.06 - 4.12: 960 4.12 - 6.19: 137 6.19 - 8.25: 53 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=" C ASP A 823 " pdb=" N VAL A 824 " pdb=" CA VAL A 824 " ideal model delta sigma weight residual 120.62 128.20 -7.58 1.64e+00 3.72e-01 2.13e+01 angle pdb=" C ALA B 474 " pdb=" N MET B 475 " pdb=" CA MET B 475 " ideal model delta sigma weight residual 121.54 130.07 -8.53 1.91e+00 2.74e-01 1.99e+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 - 0.113: 1896 0.113 - 0.226: 156 0.226 - 0.339: 6 0.339 - 0.452: 1 0.452 - 0.565: 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 -2.73 -2.17 -0.57 2.00e-01 2.50e+01 7.98e+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 -2.73 -2.32 -0.41 2.00e-01 2.50e+01 4.12e+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: 1.430 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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= 0.614 Angle : 1.430 53.073 16923 Z= 0.683 Chirality : 0.065 0.565 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/Z covalent geometry : bond 0.00871 / 0.45 (12268) covalent geometry : angle 1.17130 / 0.68 (16911) hydrogen bonds : bond 0.34558 / 23.34 ( 310) hydrogen bonds : angle 10.38654 / 7.36 ( 890) metal coordination : bond 0.78285 / 39.13 ( 4) metal coordination : angle 30.85514 / 18.45 ( 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 : 0.446 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: 0.1536 time to fit residues: 50.3072 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 : 0.425 ------------------------------------------------------------------------------- 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... B 86 GLN B 205 HIS B 229 GLN B 738 HIS A 342 ASN A 496 HIS A 631 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120998 restraints weight = 17808.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122011 restraints weight = 14458.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122848 restraints weight = 11985.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122976 restraints weight = 9028.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124301 restraints weight = 8574.878| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12272 Z= 0.148 Angle : 0.859 29.704 16923 Z= 0.381 Chirality : 0.046 0.311 2060 Planarity : 0.006 0.048 2053 Dihedral : 17.400 175.957 2060 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.15 % Allowed : 10.93 % Favored : 85.93 % 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: -5.01 (0.17), residues: 1518 helix: -3.78 (0.12), residues: 790 sheet: -2.15 (0.45), residues: 118 loop : -2.66 (0.22), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 921 TYR 0.016 0.002 TYR A 859 PHE 0.025 0.002 PHE A 879 TRP 0.021 0.002 TRP A 149 HIS 0.005 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (12268) covalent geometry : angle 0.74617 / 0.38 (16911) hydrogen bonds : bond 0.06932 / 4.93 ( 310) hydrogen bonds : angle 5.79503 / 4.05 ( 890) metal coordination : bond 0.03518 / 1.78 ( 4) metal coordination : angle 15.98015 / 9.79 ( 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 173 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7130 (t70) cc_final: 0.6866 (t0) REVERT: B 457 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (t) REVERT: B 644 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7590 (mt-10) outliers start: 32 outliers final: 15 residues processed: 166 average time/residue: 0.1098 time to fit residues: 26.5617 Evaluate side-chains 123 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 457 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 321 SER Chi-restraints excluded: chain A residue 388 SER 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 1014 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3711 r_free = 0.3711 target = 0.147055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122334 restraints weight = 18039.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123345 restraints weight = 16829.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124456 restraints weight = 13920.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124688 restraints weight = 9677.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124773 restraints weight = 10383.065| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12272 Z= 0.137 Angle : 0.775 23.162 16923 Z= 0.347 Chirality : 0.045 0.370 2060 Planarity : 0.005 0.043 2053 Dihedral : 16.931 177.177 2060 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.64 % Allowed : 12.60 % Favored : 83.76 % 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: -4.24 (0.19), residues: 1518 helix: -3.09 (0.14), residues: 792 sheet: -1.72 (0.49), residues: 114 loop : -2.41 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 924 TYR 0.014 0.002 TYR A 859 PHE 0.013 0.001 PHE B 340 TRP 0.013 0.002 TRP A 149 HIS 0.007 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12268) covalent geometry : angle 0.67997 / 0.35 (16911) hydrogen bonds : bond 0.05560 / 3.97 ( 310) hydrogen bonds : angle 4.92787 / 3.43 ( 890) metal coordination : bond 0.01251 / 0.64 ( 4) metal coordination : angle 13.97945 / 9.52 ( 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 160 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7165 (t70) cc_final: 0.6898 (t0) REVERT: B 457 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7889 (t) REVERT: B 744 GLN cc_start: 0.8031 (tp40) cc_final: 0.7789 (tp40) outliers start: 37 outliers final: 20 residues processed: 157 average time/residue: 0.0993 time to fit residues: 23.8334 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER 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 321 SER 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 1014 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 157 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119659 restraints weight = 17987.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121007 restraints weight = 15287.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122038 restraints weight = 13703.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122099 restraints weight = 9317.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122251 restraints weight = 9972.585| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12272 Z= 0.166 Angle : 0.762 23.581 16923 Z= 0.344 Chirality : 0.046 0.380 2060 Planarity : 0.005 0.044 2053 Dihedral : 16.718 176.446 2060 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.25 % Allowed : 14.37 % 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: -3.82 (0.20), residues: 1518 helix: -2.65 (0.16), residues: 791 sheet: -1.57 (0.50), residues: 114 loop : -2.34 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 167 TYR 0.015 0.002 TYR A 864 PHE 0.016 0.001 PHE B 340 TRP 0.011 0.001 TRP A 787 HIS 0.006 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (12268) covalent geometry : angle 0.67787 / 0.34 (16911) hydrogen bonds : bond 0.05043 / 3.62 ( 310) hydrogen bonds : angle 4.66005 / 3.23 ( 890) metal coordination : bond 0.00818 / 0.40 ( 4) metal coordination : angle 13.10572 / 9.18 ( 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 151 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7272 (t70) cc_final: 0.6968 (t0) REVERT: B 457 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7935 (t) REVERT: B 744 GLN cc_start: 0.8138 (tp40) cc_final: 0.7730 (tp-100) REVERT: A 27 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8475 (pp) outliers start: 33 outliers final: 23 residues processed: 146 average time/residue: 0.0972 time to fit residues: 21.4392 Evaluate side-chains 132 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 457 VAL 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 742 LEU 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 321 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 739 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 142 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 151 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3713 r_free = 0.3713 target = 0.147159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122460 restraints weight = 17870.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123753 restraints weight = 15111.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124783 restraints weight = 13611.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124841 restraints weight = 9173.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125030 restraints weight = 9620.660| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12272 Z= 0.113 Angle : 0.697 23.624 16923 Z= 0.315 Chirality : 0.043 0.347 2060 Planarity : 0.004 0.060 2053 Dihedral : 16.518 176.053 2060 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.84 % Allowed : 14.96 % Favored : 81.20 % 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: -3.30 (0.20), residues: 1518 helix: -2.16 (0.17), residues: 790 sheet: -1.40 (0.51), residues: 114 loop : -2.18 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 924 TYR 0.010 0.001 TYR A 859 PHE 0.010 0.001 PHE A 879 TRP 0.015 0.001 TRP A 629 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (12268) covalent geometry : angle 0.61740 / 0.31 (16911) hydrogen bonds : bond 0.04460 / 3.23 ( 310) hydrogen bonds : angle 4.19045 / 2.91 ( 890) metal coordination : bond 0.00469 / 0.23 ( 4) metal coordination : angle 12.20186 / 8.86 ( 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 157 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7216 (t70) cc_final: 0.6949 (t0) REVERT: A 27 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8421 (pp) outliers start: 39 outliers final: 22 residues processed: 155 average time/residue: 0.0965 time to fit residues: 22.8064 Evaluate side-chains 124 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 81 ARG 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 281 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 652 LEU 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 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 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: 4.9990 chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 chunk 154 optimal weight: 7.9990 chunk 57 optimal weight: 0.0000 chunk 69 optimal weight: 0.4980 chunk 116 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3700 r_free = 0.3700 target = 0.146112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121361 restraints weight = 17733.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122818 restraints weight = 15207.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123353 restraints weight = 12714.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123324 restraints weight = 9562.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123420 restraints weight = 9259.453| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12272 Z= 0.127 Angle : 0.697 23.228 16923 Z= 0.316 Chirality : 0.044 0.364 2060 Planarity : 0.004 0.052 2053 Dihedral : 16.421 176.023 2060 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.33 % Allowed : 15.55 % 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: -2.96 (0.21), residues: 1518 helix: -1.81 (0.18), residues: 798 sheet: -1.40 (0.51), residues: 116 loop : -2.11 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 416 TYR 0.012 0.001 TYR A 864 PHE 0.013 0.001 PHE B 340 TRP 0.012 0.001 TRP B 497 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12268) covalent geometry : angle 0.61975 / 0.31 (16911) hydrogen bonds : bond 0.04416 / 3.17 ( 310) hydrogen bonds : angle 4.05937 / 2.81 ( 890) metal coordination : bond 0.00676 / 0.33 ( 4) metal coordination : angle 11.97483 / 8.67 ( 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 155 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7330 (t70) cc_final: 0.6921 (t0) REVERT: A 27 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8406 (pp) outliers start: 44 outliers final: 26 residues processed: 150 average time/residue: 0.0906 time to fit residues: 21.1988 Evaluate side-chains 130 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 395 ILE 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 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 321 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 739 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 61 optimal weight: 0.0050 chunk 74 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3698 r_free = 0.3698 target = 0.146222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121217 restraints weight = 17778.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123263 restraints weight = 15150.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124021 restraints weight = 12450.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123868 restraints weight = 8782.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124130 restraints weight = 8527.182| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12272 Z= 0.132 Angle : 0.694 22.970 16923 Z= 0.316 Chirality : 0.044 0.364 2060 Planarity : 0.004 0.044 2053 Dihedral : 16.352 175.983 2060 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.94 % Allowed : 17.03 % Favored : 79.04 % 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: -2.69 (0.21), residues: 1518 helix: -1.55 (0.18), residues: 799 sheet: -1.38 (0.51), residues: 116 loop : -2.01 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 416 TYR 0.013 0.001 TYR A 864 PHE 0.014 0.001 PHE B 340 TRP 0.013 0.001 TRP B 497 HIS 0.006 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12268) covalent geometry : angle 0.62090 / 0.31 (16911) hydrogen bonds : bond 0.04333 / 3.12 ( 310) hydrogen bonds : angle 4.02623 / 2.79 ( 890) metal coordination : bond 0.00711 / 0.35 ( 4) metal coordination : angle 11.68941 / 8.49 ( 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 150 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 66 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 189 ASP cc_start: 0.7420 (t70) cc_final: 0.6987 (t0) REVERT: A 27 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8429 (pp) outliers start: 40 outliers final: 32 residues processed: 144 average time/residue: 0.0948 time to fit residues: 20.6036 Evaluate side-chains 138 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 66 ASN 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 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 395 ILE 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 717 VAL 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 27 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 731 LEU Chi-restraints excluded: chain A residue 739 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 144 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 102 optimal weight: 0.0050 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 154 optimal weight: 0.0070 chunk 136 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 286 GLN A 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125340 restraints weight = 17500.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128869 restraints weight = 16367.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128864 restraints weight = 9976.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128600 restraints weight = 8271.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128720 restraints weight = 7731.543| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12272 Z= 0.101 Angle : 0.654 22.393 16923 Z= 0.298 Chirality : 0.042 0.337 2060 Planarity : 0.004 0.042 2053 Dihedral : 16.222 176.091 2060 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.76 % Allowed : 18.50 % Favored : 78.74 % 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: -2.29 (0.22), residues: 1518 helix: -1.14 (0.19), residues: 785 sheet: -1.22 (0.52), residues: 115 loop : -1.93 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.008 0.001 TYR A 859 PHE 0.008 0.001 PHE A 879 TRP 0.013 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (12268) covalent geometry : angle 0.58324 / 0.30 (16911) hydrogen bonds : bond 0.04008 / 2.91 ( 310) hydrogen bonds : angle 3.77065 / 2.60 ( 890) metal coordination : bond 0.00439 / 0.22 ( 4) metal coordination : angle 11.16693 / 8.24 ( 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 150 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7307 (t70) cc_final: 0.6869 (t0) REVERT: A 430 ASP cc_start: 0.7888 (t0) cc_final: 0.7621 (t0) REVERT: A 525 TRP cc_start: 0.6984 (t60) cc_final: 0.6584 (t-100) outliers start: 28 outliers final: 19 residues processed: 143 average time/residue: 0.0929 time to fit residues: 20.4053 Evaluate side-chains 125 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 281 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 648 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=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: 0.0970 chunk 152 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3731 r_free = 0.3731 target = 0.149440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124915 restraints weight = 17442.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127050 restraints weight = 15591.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127803 restraints weight = 12714.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127571 restraints weight = 9084.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127719 restraints weight = 8806.070| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12272 Z= 0.116 Angle : 0.678 22.170 16923 Z= 0.307 Chirality : 0.043 0.354 2060 Planarity : 0.004 0.040 2053 Dihedral : 16.158 176.966 2058 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.95 % Allowed : 18.70 % 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: -2.11 (0.22), residues: 1518 helix: -0.96 (0.19), residues: 792 sheet: -1.19 (0.52), residues: 115 loop : -1.91 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 416 TYR 0.010 0.001 TYR A 864 PHE 0.012 0.001 PHE B 340 TRP 0.013 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (12268) covalent geometry : angle 0.60827 / 0.31 (16911) hydrogen bonds : bond 0.04038 / 2.92 ( 310) hydrogen bonds : angle 3.78922 / 2.62 ( 890) metal coordination : bond 0.00635 / 0.31 ( 4) metal coordination : angle 11.25090 / 8.21 ( 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 146 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7309 (t70) cc_final: 0.6858 (t0) REVERT: B 582 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8648 (tp) REVERT: A 430 ASP cc_start: 0.7893 (t0) cc_final: 0.7622 (t0) REVERT: A 525 TRP cc_start: 0.7030 (t60) cc_final: 0.6631 (t-100) outliers start: 30 outliers final: 24 residues processed: 138 average time/residue: 0.0881 time to fit residues: 19.2114 Evaluate side-chains 135 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 246 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 825 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 606 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 731 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: 2.9990 chunk 36 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3728 r_free = 0.3728 target = 0.149167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124888 restraints weight = 17688.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125436 restraints weight = 17265.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126365 restraints weight = 14682.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126538 restraints weight = 11623.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126695 restraints weight = 10620.006| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12272 Z= 0.119 Angle : 0.681 22.588 16923 Z= 0.307 Chirality : 0.043 0.356 2060 Planarity : 0.004 0.040 2053 Dihedral : 16.106 177.264 2058 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.76 % Allowed : 18.90 % 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: -2.02 (0.22), residues: 1518 helix: -0.85 (0.19), residues: 802 sheet: -1.22 (0.51), residues: 117 loop : -1.91 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 416 TYR 0.010 0.001 TYR A 864 PHE 0.012 0.001 PHE B 340 TRP 0.014 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12268) covalent geometry : angle 0.61118 / 0.31 (16911) hydrogen bonds : bond 0.04004 / 2.89 ( 310) hydrogen bonds : angle 3.76909 / 2.61 ( 890) metal coordination : bond 0.00668 / 0.33 ( 4) metal coordination : angle 11.32047 / 8.28 ( 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 138 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7289 (t70) cc_final: 0.6837 (t0) REVERT: B 582 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8651 (tp) REVERT: A 430 ASP cc_start: 0.7848 (t0) cc_final: 0.7589 (t0) REVERT: A 525 TRP cc_start: 0.7080 (t60) cc_final: 0.6741 (t-100) outliers start: 28 outliers final: 23 residues processed: 132 average time/residue: 0.0911 time to fit residues: 18.9838 Evaluate side-chains 131 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 246 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 582 LEU 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 719 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 826 VAL 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 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: 3.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 151 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.148094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123352 restraints weight = 17509.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125427 restraints weight = 16108.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126061 restraints weight = 12627.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125980 restraints weight = 8940.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126157 restraints weight = 8845.353| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12272 Z= 0.136 Angle : 0.703 23.110 16923 Z= 0.317 Chirality : 0.044 0.366 2060 Planarity : 0.004 0.039 2053 Dihedral : 16.081 177.674 2058 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.05 % Allowed : 18.80 % Favored : 78.15 % 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: -1.97 (0.22), residues: 1518 helix: -0.78 (0.19), residues: 802 sheet: -1.26 (0.51), residues: 117 loop : -1.93 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 416 TYR 0.011 0.001 TYR A 864 PHE 0.014 0.001 PHE B 340 TRP 0.013 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (12268) covalent geometry : angle 0.63302 / 0.32 (16911) hydrogen bonds : bond 0.04075 / 2.93 ( 310) hydrogen bonds : angle 3.82196 / 2.65 ( 890) metal coordination : bond 0.00818 / 0.40 ( 4) metal coordination : angle 11.45773 / 8.38 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1749.88 seconds wall clock time: 30 minutes 56.73 seconds (1856.73 seconds total)