Starting phenix.real_space_refine on Wed Jul 30 05:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ppr_20446/07_2025/6ppr_20446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppr_20446/07_2025/6ppr_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_20446/07_2025/6ppr_20446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppr_20446/07_2025/6ppr_20446.map" model { file = "/net/cci-nas-00/data/ceres_data/6ppr_20446/07_2025/6ppr_20446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppr_20446/07_2025/6ppr_20446_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 14, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 20, 'ARG:plan': 8} 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: {'GLN:plan1': 10, 'ASP:plan': 25, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 34, 'ARG:plan': 25} 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: 7.73, per 1000 atoms: 0.64 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: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.53 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: 3.85 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4966 1.42 - 1.64: 7232 1.64 - 1.85: 58 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12268 Sorted by residual: bond pdb=" N3B ANP A1101 " pdb=" PG ANP A1101 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP A1101 " pdb=" PB ANP A1101 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ARG B 385 " pdb=" CA ARG B 385 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N VAL A 904 " pdb=" CA VAL A 904 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.18e-02 7.18e+03 9.71e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15768 2.06 - 4.12: 937 4.12 - 6.19: 131 6.19 - 8.25: 52 8.25 - 10.31: 23 Bond angle restraints: 16911 Sorted by residual: angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" CB PRO B 208 " ideal model delta sigma weight residual 103.25 111.33 -8.08 1.05e+00 9.07e-01 5.92e+01 angle pdb=" N PRO B 211 " pdb=" CA PRO B 211 " pdb=" CB PRO B 211 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" N VAL B 756 " pdb=" CA VAL B 756 " pdb=" C VAL B 756 " ideal model delta sigma weight residual 112.29 107.04 5.25 9.40e-01 1.13e+00 3.12e+01 angle pdb=" C4' DC X 5 " pdb=" C3' DC X 5 " pdb=" O3' DC X 5 " ideal model delta sigma weight residual 110.00 117.53 -7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C4' DG X 12 " pdb=" C3' DG X 12 " pdb=" O3' DG X 12 " ideal model delta sigma weight residual 110.00 117.06 -7.06 1.50e+00 4.44e-01 2.22e+01 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 7022 35.43 - 70.87: 156 70.87 - 106.30: 11 106.30 - 141.73: 0 141.73 - 177.17: 6 Dihedral angle restraints: 7195 sinusoidal: 2669 harmonic: 4526 Sorted by residual: dihedral pdb=" CA LEU B 134 " pdb=" C LEU B 134 " pdb=" N PRO B 135 " pdb=" CA PRO B 135 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TYR A 859 " pdb=" C TYR A 859 " pdb=" N ASP A 860 " pdb=" CA ASP A 860 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLU A 814 " pdb=" C GLU A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 7192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1831 0.099 - 0.198: 214 0.198 - 0.297: 13 0.297 - 0.396: 1 0.396 - 0.495: 1 Chirality restraints: 2060 Sorted by residual: chirality pdb=" C3' DC X 5 " pdb=" C4' DC X 5 " pdb=" O3' DC X 5 " pdb=" C2' DC X 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C3' DG X 12 " pdb=" C4' DG X 12 " pdb=" O3' DG X 12 " pdb=" C2' DG X 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' ANP A1101 " pdb=" C2' ANP A1101 " pdb=" C4' ANP A1101 " pdb=" O3' ANP A1101 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2057 not shown) Planarity restraints: 2053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 261 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA B 261 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 261 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 348 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO B 349 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 807 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 808 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 808 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 808 " -0.041 5.00e-02 4.00e+02 ... (remaining 2050 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 86 2.61 - 3.18: 9331 3.18 - 3.75: 17014 3.75 - 4.33: 23114 4.33 - 4.90: 37601 Nonbonded interactions: 87146 Sorted by model distance: nonbonded pdb=" N2 DG X 12 " pdb=" O2 DC X 43 " model vdw 2.032 2.496 nonbonded pdb=" N GLU B 642 " pdb=" OE1 GLU B 642 " model vdw 2.078 3.120 nonbonded pdb=" CG2 VAL B 641 " pdb=" OE1 GLU B 642 " model vdw 2.113 3.460 nonbonded pdb=" CD1 LEU A 27 " pdb=" CA ALA A 281 " model vdw 2.202 3.890 nonbonded pdb=" OH TYR A 956 " pdb=" OP1 DT X 1 " model vdw 2.257 3.040 ... (remaining 87141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.200 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.150 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.817 12272 Z= 0.590 Angle : 1.422 53.073 16923 Z= 0.652 Chirality : 0.063 0.495 2060 Planarity : 0.008 0.076 2053 Dihedral : 15.432 177.166 4243 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.14 % Favored : 89.79 % Rotamer: Outliers : 1.28 % Allowed : 6.10 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.039 0.004 TRP B 864 HIS 0.014 0.002 HIS B 243 PHE 0.022 0.003 PHE A 618 TYR 0.027 0.003 TYR B 342 ARG 0.017 0.001 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.34558 ( 310) hydrogen bonds : angle 10.38654 ( 890) metal coordination : bond 0.78285 ( 4) metal coordination : angle 30.85514 ( 12) covalent geometry : bond 0.00865 (12268) covalent geometry : angle 1.16157 (16911) *********************** 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 : 1.280 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: 0.3343 time to fit residues: 108.3578 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 : 1.114 ------------------------------------------------------------------------------- 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 136 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 0.0670 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.0370 chunk 147 optimal weight: 0.9980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 205 HIS B 229 GLN B 738 HIS ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 ASN A 631 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124015 restraints weight = 17804.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123885 restraints weight = 15442.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125070 restraints weight = 13401.922| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12272 Z= 0.128 Angle : 0.756 24.222 16923 Z= 0.344 Chirality : 0.042 0.236 2060 Planarity : 0.006 0.048 2053 Dihedral : 16.935 177.134 2060 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.35 % Allowed : 11.02 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.18), residues: 1518 helix: -3.67 (0.12), residues: 790 sheet: -1.97 (0.47), residues: 117 loop : -2.51 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 409 HIS 0.007 0.001 HIS B 243 PHE 0.011 0.001 PHE B 622 TYR 0.015 0.002 TYR A 956 ARG 0.004 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 310) hydrogen bonds : angle 5.19931 ( 890) metal coordination : bond 0.01597 ( 4) metal coordination : angle 13.61845 ( 12) covalent geometry : bond 0.00272 (12268) covalent geometry : angle 0.66312 (16911) *********************** 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 189 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7150 (t70) cc_final: 0.6854 (t0) REVERT: B 644 GLU cc_start: 0.7746 (tt0) cc_final: 0.7449 (mt-10) REVERT: B 744 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7828 (tp-100) outliers start: 34 outliers final: 14 residues processed: 181 average time/residue: 0.2376 time to fit residues: 61.8861 Evaluate side-chains 126 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 156 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 111 optimal weight: 0.0870 chunk 158 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 304 HIS A 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125087 restraints weight = 17881.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127742 restraints weight = 14984.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128182 restraints weight = 12246.627| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12272 Z= 0.112 Angle : 0.692 22.365 16923 Z= 0.313 Chirality : 0.041 0.199 2060 Planarity : 0.004 0.040 2053 Dihedral : 16.406 178.275 2060 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.15 % Allowed : 13.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.19), residues: 1518 helix: -2.86 (0.15), residues: 796 sheet: -1.52 (0.51), residues: 113 loop : -2.26 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 149 HIS 0.005 0.001 HIS A 259 PHE 0.011 0.001 PHE A 879 TYR 0.015 0.001 TYR A 956 ARG 0.005 0.000 ARG A 167 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 310) hydrogen bonds : angle 4.39627 ( 890) metal coordination : bond 0.00765 ( 4) metal coordination : angle 12.29732 ( 12) covalent geometry : bond 0.00249 (12268) covalent geometry : angle 0.60951 (16911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3036 Ramachandran restraints generated. 1518 Oldfield, 0 Emsley, 1518 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7112 (t70) cc_final: 0.6838 (t0) REVERT: A 27 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8488 (pp) outliers start: 32 outliers final: 17 residues processed: 155 average time/residue: 0.2099 time to fit residues: 50.0766 Evaluate side-chains 130 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain B residue 281 VAL 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 737 ASP Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 801 LEU 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 126 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 0.0060 chunk 110 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 124 optimal weight: 0.0000 chunk 155 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 286 GLN A 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126777 restraints weight = 17639.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127554 restraints weight = 15806.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.128401 restraints weight = 14127.082| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12272 Z= 0.101 Angle : 0.642 20.278 16923 Z= 0.293 Chirality : 0.040 0.207 2060 Planarity : 0.004 0.059 2053 Dihedral : 16.233 179.693 2060 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.95 % Allowed : 13.98 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.20), residues: 1518 helix: -2.21 (0.17), residues: 794 sheet: -1.41 (0.51), residues: 115 loop : -1.97 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.009 0.001 PHE A 879 TYR 0.009 0.001 TYR A 864 ARG 0.005 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 310) hydrogen bonds : angle 3.89553 ( 890) metal coordination : bond 0.00496 ( 4) metal coordination : angle 11.19392 ( 12) covalent geometry : bond 0.00220 (12268) covalent geometry : angle 0.56916 (16911) *********************** 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 166 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7060 (t70) cc_final: 0.6727 (t0) REVERT: A 525 TRP cc_start: 0.7049 (t60) cc_final: 0.6651 (t-100) outliers start: 30 outliers final: 17 residues processed: 157 average time/residue: 0.2342 time to fit residues: 54.2235 Evaluate side-chains 129 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 81 ARG 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 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 742 LEU 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 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 0.0000 chunk 126 optimal weight: 5.9990 chunk 94 optimal weight: 0.0170 chunk 152 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 57 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127650 restraints weight = 17735.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.129261 restraints weight = 15568.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.129799 restraints weight = 12404.092| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12272 Z= 0.096 Angle : 0.624 19.152 16923 Z= 0.284 Chirality : 0.039 0.212 2060 Planarity : 0.004 0.049 2053 Dihedral : 15.993 178.129 2058 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.44 % Allowed : 15.55 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.21), residues: 1518 helix: -1.60 (0.18), residues: 787 sheet: -1.17 (0.54), residues: 115 loop : -1.89 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 787 HIS 0.006 0.001 HIS A 304 PHE 0.016 0.001 PHE B 68 TYR 0.010 0.001 TYR B 553 ARG 0.006 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 310) hydrogen bonds : angle 3.62520 ( 890) metal coordination : bond 0.00466 ( 4) metal coordination : angle 10.55100 ( 12) covalent geometry : bond 0.00214 (12268) covalent geometry : angle 0.55690 (16911) *********************** 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 166 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.6965 (t70) cc_final: 0.6617 (t0) REVERT: B 497 TRP cc_start: 0.7800 (p90) cc_final: 0.7568 (p90) REVERT: A 430 ASP cc_start: 0.7903 (t0) cc_final: 0.7558 (t0) REVERT: A 525 TRP cc_start: 0.7036 (t60) cc_final: 0.6673 (t-100) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 0.1927 time to fit residues: 47.1667 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 ARG Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 738 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 150 optimal weight: 0.0870 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 342 ASN A 358 HIS A 631 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.149177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.124809 restraints weight = 17738.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125436 restraints weight = 15716.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126570 restraints weight = 15492.115| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12272 Z= 0.138 Angle : 0.683 21.859 16923 Z= 0.309 Chirality : 0.042 0.190 2060 Planarity : 0.004 0.054 2053 Dihedral : 15.956 176.655 2058 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.64 % Allowed : 16.14 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1518 helix: -1.38 (0.18), residues: 806 sheet: -1.18 (0.52), residues: 117 loop : -1.86 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.015 0.001 PHE B 340 TYR 0.015 0.002 TYR A 864 ARG 0.006 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 310) hydrogen bonds : angle 3.82381 ( 890) metal coordination : bond 0.00721 ( 4) metal coordination : angle 11.15233 ( 12) covalent geometry : bond 0.00327 (12268) covalent geometry : angle 0.61513 (16911) *********************** 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 147 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7213 (t70) cc_final: 0.6814 (t0) REVERT: A 430 ASP cc_start: 0.7926 (t0) cc_final: 0.7546 (t0) REVERT: A 525 TRP cc_start: 0.7106 (t60) cc_final: 0.6688 (t-100) outliers start: 37 outliers final: 24 residues processed: 142 average time/residue: 0.2083 time to fit residues: 45.9789 Evaluate side-chains 130 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 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 742 LEU 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 738 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 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 23 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123957 restraints weight = 17651.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125829 restraints weight = 16353.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126366 restraints weight = 12975.698| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12272 Z= 0.121 Angle : 0.669 23.910 16923 Z= 0.300 Chirality : 0.041 0.193 2060 Planarity : 0.004 0.047 2053 Dihedral : 15.830 177.260 2058 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.05 % Allowed : 17.13 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.22), residues: 1518 helix: -1.05 (0.19), residues: 804 sheet: -1.17 (0.52), residues: 117 loop : -1.83 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.012 0.001 PHE B 340 TYR 0.013 0.001 TYR A 864 ARG 0.005 0.000 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 310) hydrogen bonds : angle 3.71097 ( 890) metal coordination : bond 0.00617 ( 4) metal coordination : angle 11.55187 ( 12) covalent geometry : bond 0.00285 (12268) covalent geometry : angle 0.59391 (16911) *********************** 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 145 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7252 (t70) cc_final: 0.6842 (t0) REVERT: A 430 ASP cc_start: 0.7833 (t0) cc_final: 0.7488 (t0) REVERT: A 525 TRP cc_start: 0.7069 (t60) cc_final: 0.6686 (t-100) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.1898 time to fit residues: 41.3063 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 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 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 LEU 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 632 MET 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 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 157 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 631 ASN A 643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121220 restraints weight = 17615.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122993 restraints weight = 15998.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123687 restraints weight = 13099.554| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12272 Z= 0.159 Angle : 0.720 25.588 16923 Z= 0.323 Chirality : 0.043 0.193 2060 Planarity : 0.004 0.042 2053 Dihedral : 15.892 177.330 2058 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.74 % Allowed : 16.63 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.22), residues: 1518 helix: -1.04 (0.19), residues: 804 sheet: -1.18 (0.51), residues: 117 loop : -1.87 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.017 0.001 PHE B 340 TYR 0.016 0.002 TYR A 864 ARG 0.003 0.000 ARG B 587 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 310) hydrogen bonds : angle 3.92901 ( 890) metal coordination : bond 0.00888 ( 4) metal coordination : angle 12.05982 ( 12) covalent geometry : bond 0.00382 (12268) covalent geometry : angle 0.64476 (16911) *********************** 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 147 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7453 (t70) cc_final: 0.6973 (t0) REVERT: A 430 ASP cc_start: 0.7856 (t0) cc_final: 0.7498 (t0) REVERT: A 525 TRP cc_start: 0.7122 (t60) cc_final: 0.6720 (t-100) outliers start: 38 outliers final: 28 residues processed: 139 average time/residue: 0.2162 time to fit residues: 46.5789 Evaluate side-chains 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 LEU 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 632 MET 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 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 156 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 157 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124388 restraints weight = 17465.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126643 restraints weight = 15795.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127264 restraints weight = 11916.926| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12272 Z= 0.106 Angle : 0.659 23.551 16923 Z= 0.297 Chirality : 0.040 0.211 2060 Planarity : 0.004 0.042 2053 Dihedral : 15.763 177.238 2058 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.25 % Allowed : 17.13 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.22), residues: 1518 helix: -0.70 (0.19), residues: 801 sheet: -1.11 (0.52), residues: 117 loop : -1.79 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 787 HIS 0.004 0.001 HIS A 259 PHE 0.011 0.001 PHE B 68 TYR 0.009 0.001 TYR A 864 ARG 0.004 0.000 ARG B 822 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 310) hydrogen bonds : angle 3.64128 ( 890) metal coordination : bond 0.00442 ( 4) metal coordination : angle 11.22870 ( 12) covalent geometry : bond 0.00243 (12268) covalent geometry : angle 0.58706 (16911) *********************** 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 148 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7336 (t70) cc_final: 0.6907 (t0) REVERT: A 430 ASP cc_start: 0.7867 (t0) cc_final: 0.7547 (t0) REVERT: A 525 TRP cc_start: 0.7082 (t60) cc_final: 0.6705 (t-100) REVERT: A 801 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8754 (tm) outliers start: 33 outliers final: 25 residues processed: 140 average time/residue: 0.1894 time to fit residues: 41.8839 Evaluate side-chains 136 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 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 742 LEU 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 632 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120936 restraints weight = 17443.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121366 restraints weight = 15198.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.122492 restraints weight = 13905.459| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12272 Z= 0.160 Angle : 0.719 25.519 16923 Z= 0.322 Chirality : 0.043 0.205 2060 Planarity : 0.004 0.041 2053 Dihedral : 15.848 177.157 2058 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.85 % Allowed : 17.62 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1518 helix: -0.75 (0.19), residues: 801 sheet: -1.18 (0.51), residues: 117 loop : -1.79 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.017 0.001 PHE B 340 TYR 0.016 0.002 TYR A 864 ARG 0.006 0.000 ARG B 822 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 310) hydrogen bonds : angle 3.85756 ( 890) metal coordination : bond 0.00891 ( 4) metal coordination : angle 12.08307 ( 12) covalent geometry : bond 0.00384 (12268) covalent geometry : angle 0.64343 (16911) ********************** 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 134 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: A 430 ASP cc_start: 0.7870 (t0) cc_final: 0.7510 (t0) REVERT: A 525 TRP cc_start: 0.7109 (t60) cc_final: 0.6707 (t-100) REVERT: A 855 ASP cc_start: 0.8090 (t0) cc_final: 0.7869 (m-30) outliers start: 29 outliers final: 26 residues processed: 128 average time/residue: 0.1876 time to fit residues: 37.8885 Evaluate side-chains 130 residues out of total 1233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 LEU 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 632 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 0.0060 chunk 10 optimal weight: 0.0670 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 0.1980 chunk 116 optimal weight: 0.0000 chunk 153 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 95 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.0938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS A 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.154210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130407 restraints weight = 17471.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131884 restraints weight = 15038.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132602 restraints weight = 12900.075| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12272 Z= 0.101 Angle : 0.640 21.563 16923 Z= 0.292 Chirality : 0.039 0.234 2060 Planarity : 0.004 0.042 2053 Dihedral : 15.622 176.805 2058 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 18.90 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1518 helix: -0.20 (0.20), residues: 789 sheet: -1.16 (0.51), residues: 119 loop : -1.67 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.010 0.001 PHE B 68 TYR 0.009 0.001 TYR B 553 ARG 0.018 0.000 ARG B 822 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 310) hydrogen bonds : angle 3.37843 ( 890) metal coordination : bond 0.00504 ( 4) metal coordination : angle 10.71950 ( 12) covalent geometry : bond 0.00221 (12268) covalent geometry : angle 0.57303 (16911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.84 seconds wall clock time: 60 minutes 38.51 seconds (3638.51 seconds total)