Starting phenix.real_space_refine on Thu Sep 26 03:43:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/09_2024/6ppr_20446_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/09_2024/6ppr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/09_2024/6ppr_20446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/09_2024/6ppr_20446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/09_2024/6ppr_20446_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppr_20446/09_2024/6ppr_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-5461/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: 7.26, per 1000 atoms: 0.61 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: 2.85 Conformation dependent library (CDL) restraints added in 1.6 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: 3.59 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: 3.54 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4966 1.42 - 1.64: 7232 1.64 - 1.85: 58 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12268 Sorted by residual: bond pdb=" N3B ANP A1101 " pdb=" PG ANP A1101 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O3A ANP A1101 " pdb=" PB ANP A1101 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ARG B 385 " pdb=" CA ARG B 385 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N VAL A 904 " pdb=" CA VAL A 904 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.18e-02 7.18e+03 9.71e+00 ... (remaining 12263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15768 2.06 - 4.12: 937 4.12 - 6.19: 131 6.19 - 8.25: 52 8.25 - 10.31: 23 Bond angle restraints: 16911 Sorted by residual: angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" CB PRO B 208 " ideal model delta sigma weight residual 103.25 111.33 -8.08 1.05e+00 9.07e-01 5.92e+01 angle pdb=" N PRO B 211 " pdb=" CA PRO B 211 " pdb=" CB PRO B 211 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" N VAL B 756 " pdb=" CA VAL B 756 " pdb=" C VAL B 756 " ideal model delta sigma weight residual 112.29 107.04 5.25 9.40e-01 1.13e+00 3.12e+01 angle pdb=" C4' DC X 5 " pdb=" C3' DC X 5 " pdb=" O3' DC X 5 " ideal model delta sigma weight residual 110.00 117.53 -7.53 1.50e+00 4.44e-01 2.52e+01 angle pdb=" C4' DG X 12 " pdb=" C3' DG X 12 " pdb=" O3' DG X 12 " ideal model delta sigma weight residual 110.00 117.06 -7.06 1.50e+00 4.44e-01 2.22e+01 ... (remaining 16906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 7022 35.43 - 70.87: 156 70.87 - 106.30: 11 106.30 - 141.73: 0 141.73 - 177.17: 6 Dihedral angle restraints: 7195 sinusoidal: 2669 harmonic: 4526 Sorted by residual: dihedral pdb=" CA LEU B 134 " pdb=" C LEU B 134 " pdb=" N PRO B 135 " pdb=" CA PRO B 135 " ideal model delta harmonic sigma weight residual -180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA TYR A 859 " pdb=" C TYR A 859 " pdb=" N ASP A 860 " pdb=" CA ASP A 860 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLU A 814 " pdb=" C GLU A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 7192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1831 0.099 - 0.198: 214 0.198 - 0.297: 13 0.297 - 0.396: 1 0.396 - 0.495: 1 Chirality restraints: 2060 Sorted by residual: chirality pdb=" C3' DC X 5 " pdb=" C4' DC X 5 " pdb=" O3' DC X 5 " pdb=" C2' DC X 5 " both_signs ideal model delta sigma weight residual False -2.66 -2.17 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C3' DG X 12 " pdb=" C4' DG X 12 " pdb=" O3' DG X 12 " pdb=" C2' DG X 12 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' ANP A1101 " pdb=" C2' ANP A1101 " pdb=" C4' ANP A1101 " pdb=" O3' ANP A1101 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2057 not shown) Planarity restraints: 2053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 261 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ALA B 261 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 261 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 348 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO B 349 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 349 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 349 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 807 " -0.048 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO A 808 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 808 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 808 " -0.041 5.00e-02 4.00e+02 ... (remaining 2050 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 86 2.61 - 3.18: 9331 3.18 - 3.75: 17014 3.75 - 4.33: 23114 4.33 - 4.90: 37601 Nonbonded interactions: 87146 Sorted by model distance: nonbonded pdb=" N2 DG X 12 " pdb=" O2 DC X 43 " model vdw 2.032 2.496 nonbonded pdb=" N GLU B 642 " pdb=" OE1 GLU B 642 " model vdw 2.078 3.120 nonbonded pdb=" CG2 VAL B 641 " pdb=" OE1 GLU B 642 " model vdw 2.113 3.460 nonbonded pdb=" CD1 LEU A 27 " pdb=" CA ALA A 281 " model vdw 2.202 3.890 nonbonded pdb=" OH TYR A 956 " pdb=" OP1 DT X 1 " model vdw 2.257 3.040 ... (remaining 87141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.670 Find NCS groups from input model: 0.220 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.530 ------------------------------------------------------------------------------- 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 : 0.009 0.161 12268 Z= 0.564 Angle : 1.162 10.312 16911 Z= 0.649 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 *********************** 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 fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 1.244 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: 0.3342 time to fit residues: 107.8219 Evaluate side-chains 120 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12268 Z= 0.179 Angle : 0.663 8.750 16911 Z= 0.342 Chirality : 0.042 0.238 2060 Planarity : 0.006 0.048 2053 Dihedral : 16.940 177.100 2060 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.44 % Allowed : 10.83 % Favored : 85.73 % 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 0.001 TYR A 956 ARG 0.004 0.000 ARG B 178 *********************** 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 fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7237 (t70) cc_final: 0.6927 (t0) REVERT: B 644 GLU cc_start: 0.7815 (tt0) cc_final: 0.7504 (mt-10) REVERT: B 744 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7765 (tp-100) outliers start: 35 outliers final: 14 residues processed: 181 average time/residue: 0.2282 time to fit residues: 59.6864 Evaluate side-chains 128 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 81 optimal weight: 0.0870 chunk 45 optimal weight: 4.9990 chunk 122 optimal weight: 0.0170 chunk 100 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 0.0270 chunk 159 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 overall best weight: 0.2254 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12268 Z= 0.154 Angle : 0.599 9.014 16911 Z= 0.307 Chirality : 0.040 0.212 2060 Planarity : 0.004 0.040 2053 Dihedral : 16.379 178.413 2060 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.95 % Allowed : 13.09 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.19), residues: 1518 helix: -2.83 (0.15), residues: 793 sheet: -1.46 (0.52), residues: 113 loop : -2.17 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 787 HIS 0.004 0.001 HIS A 259 PHE 0.010 0.001 PHE A 879 TYR 0.015 0.001 TYR A 956 ARG 0.003 0.000 ARG A 167 *********************** 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 170 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7185 (t70) cc_final: 0.6901 (t0) REVERT: A 27 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8346 (pp) outliers start: 30 outliers final: 16 residues processed: 164 average time/residue: 0.2050 time to fit residues: 50.5493 Evaluate side-chains 129 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 145 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 0.1980 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 770 HIS B 839 HIS A 286 GLN A 304 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12268 Z= 0.165 Angle : 0.587 9.709 16911 Z= 0.300 Chirality : 0.040 0.215 2060 Planarity : 0.004 0.061 2053 Dihedral : 16.265 179.783 2060 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.15 % Allowed : 14.07 % Favored : 82.78 % 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: -3.32 (0.20), residues: 1518 helix: -2.28 (0.16), residues: 800 sheet: -1.35 (0.52), residues: 115 loop : -2.03 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.010 0.001 PHE B 340 TYR 0.012 0.001 TYR A 864 ARG 0.005 0.000 ARG B 416 *********************** 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 158 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7290 (t70) cc_final: 0.6929 (t0) REVERT: A 27 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 382 MET cc_start: 0.8230 (mtm) cc_final: 0.7983 (mtt) outliers start: 32 outliers final: 18 residues processed: 151 average time/residue: 0.2246 time to fit residues: 50.1833 Evaluate side-chains 129 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 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 742 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 140 optimal weight: 0.0040 chunk 39 optimal weight: 6.9990 overall best weight: 2.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 839 HIS A 342 ASN A 358 HIS A 643 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12268 Z= 0.349 Angle : 0.700 13.401 16911 Z= 0.352 Chirality : 0.046 0.201 2060 Planarity : 0.005 0.053 2053 Dihedral : 16.374 178.560 2060 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.43 % Allowed : 15.35 % 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: -3.19 (0.21), residues: 1518 helix: -2.12 (0.17), residues: 805 sheet: -1.38 (0.51), residues: 118 loop : -2.02 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 787 HIS 0.008 0.001 HIS A 304 PHE 0.021 0.002 PHE B 340 TYR 0.020 0.002 TYR A 864 ARG 0.006 0.001 ARG B 416 *********************** 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 153 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 108 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7580 (t70) cc_final: 0.7139 (t0) REVERT: B 333 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7744 (mm) REVERT: B 822 ARG cc_start: 0.5901 (mtp180) cc_final: 0.5398 (mtp180) outliers start: 45 outliers final: 24 residues processed: 144 average time/residue: 0.2060 time to fit residues: 45.2811 Evaluate side-chains 125 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 737 ASP 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 731 LEU 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 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12268 Z= 0.188 Angle : 0.610 11.636 16911 Z= 0.309 Chirality : 0.041 0.185 2060 Planarity : 0.004 0.043 2053 Dihedral : 16.142 177.593 2058 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.25 % Allowed : 16.14 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.78 (0.21), residues: 1518 helix: -1.70 (0.18), residues: 806 sheet: -1.21 (0.52), residues: 115 loop : -1.98 (0.25), residues: 597 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 0.012 0.001 PHE B 68 TYR 0.012 0.001 TYR A 864 ARG 0.003 0.000 ARG B 416 *********************** 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 150 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7475 (t70) cc_final: 0.7000 (t0) REVERT: B 285 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6968 (m-30) REVERT: A 430 ASP cc_start: 0.8062 (t0) cc_final: 0.7781 (t0) outliers start: 33 outliers final: 22 residues processed: 143 average time/residue: 0.1810 time to fit residues: 40.0453 Evaluate side-chains 131 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 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 151 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 114 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12268 Z= 0.238 Angle : 0.643 12.176 16911 Z= 0.323 Chirality : 0.043 0.212 2060 Planarity : 0.004 0.043 2053 Dihedral : 16.033 177.620 2058 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.04 % Allowed : 16.24 % Favored : 79.72 % 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: -2.61 (0.21), residues: 1518 helix: -1.49 (0.18), residues: 804 sheet: -1.24 (0.51), residues: 117 loop : -1.99 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.005 0.000 ARG B 416 *********************** 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 151 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7536 (t70) cc_final: 0.7026 (t0) REVERT: B 285 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: A 430 ASP cc_start: 0.8030 (t0) cc_final: 0.7698 (t0) REVERT: A 525 TRP cc_start: 0.6971 (t60) cc_final: 0.6511 (t-100) REVERT: A 855 ASP cc_start: 0.8171 (t0) cc_final: 0.7926 (m-30) outliers start: 41 outliers final: 27 residues processed: 140 average time/residue: 0.1999 time to fit residues: 42.9023 Evaluate side-chains 128 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 589 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 814 GLU 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 96 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 142 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12268 Z= 0.216 Angle : 0.623 11.789 16911 Z= 0.313 Chirality : 0.042 0.180 2060 Planarity : 0.004 0.044 2053 Dihedral : 15.878 177.725 2058 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.64 % Allowed : 17.13 % Favored : 79.23 % 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: -2.43 (0.22), residues: 1518 helix: -1.27 (0.19), residues: 804 sheet: -1.27 (0.51), residues: 117 loop : -2.01 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.012 0.001 PHE B 340 TYR 0.013 0.002 TYR A 864 ARG 0.002 0.000 ARG B 416 *********************** 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 143 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 189 ASP cc_start: 0.7532 (t70) cc_final: 0.7016 (t0) REVERT: B 285 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: B 497 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7773 (p90) REVERT: A 430 ASP cc_start: 0.8039 (t0) cc_final: 0.7781 (t0) REVERT: A 525 TRP cc_start: 0.6979 (t60) cc_final: 0.6541 (t-100) REVERT: A 855 ASP cc_start: 0.8168 (t0) cc_final: 0.7927 (m-30) outliers start: 37 outliers final: 28 residues processed: 136 average time/residue: 0.2001 time to fit residues: 42.0432 Evaluate side-chains 132 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 677 VAL Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 687 SER Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 633 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 2.9990 chunk 136 optimal weight: 0.0970 chunk 145 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.0060 chunk 44 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12268 Z= 0.174 Angle : 0.593 10.970 16911 Z= 0.300 Chirality : 0.041 0.175 2060 Planarity : 0.004 0.042 2053 Dihedral : 15.715 177.446 2058 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.35 % Allowed : 17.62 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.22), residues: 1518 helix: -0.98 (0.19), residues: 800 sheet: -1.22 (0.51), residues: 117 loop : -1.89 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.011 0.001 PHE B 68 TYR 0.010 0.001 TYR A 864 ARG 0.002 0.000 ARG A 871 *********************** 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 fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: A 430 ASP cc_start: 0.8023 (t0) cc_final: 0.7702 (t0) REVERT: A 525 TRP cc_start: 0.6940 (t60) cc_final: 0.6592 (t-100) REVERT: A 801 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8784 (tm) REVERT: A 855 ASP cc_start: 0.8142 (t0) cc_final: 0.7915 (m-30) outliers start: 34 outliers final: 23 residues processed: 141 average time/residue: 0.2058 time to fit residues: 44.3703 Evaluate side-chains 131 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 355 THR 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 825 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 102 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 839 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12268 Z= 0.161 Angle : 0.593 9.720 16911 Z= 0.298 Chirality : 0.040 0.208 2060 Planarity : 0.004 0.041 2053 Dihedral : 15.595 177.168 2058 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.36 % Allowed : 18.60 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.19), residues: 800 sheet: -1.21 (0.51), residues: 119 loop : -1.78 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 787 HIS 0.005 0.001 HIS A 259 PHE 0.010 0.001 PHE B 68 TYR 0.010 0.001 TYR A 859 ARG 0.002 0.000 ARG B 354 ********************** 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 143 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: A 430 ASP cc_start: 0.8015 (t0) cc_final: 0.7713 (t0) REVERT: A 525 TRP cc_start: 0.6942 (t60) cc_final: 0.6610 (t-100) REVERT: A 801 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (tm) outliers start: 24 outliers final: 20 residues processed: 138 average time/residue: 0.2182 time to fit residues: 45.4193 Evaluate side-chains 133 residues out of total 1233 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 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 684 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 633 ILE 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 136 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 18 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** B 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 839 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127609 restraints weight = 17348.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129742 restraints weight = 16142.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130408 restraints weight = 12104.602| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12268 Z= 0.149 Angle : 0.574 9.610 16911 Z= 0.290 Chirality : 0.040 0.219 2060 Planarity : 0.004 0.040 2053 Dihedral : 15.514 176.998 2058 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.66 % Allowed : 18.11 % Favored : 79.23 % 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: -1.52 (0.22), residues: 1518 helix: -0.43 (0.20), residues: 795 sheet: -1.15 (0.51), residues: 119 loop : -1.64 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 325 HIS 0.005 0.001 HIS A 259 PHE 0.010 0.001 PHE B 68 TYR 0.008 0.001 TYR A 859 ARG 0.002 0.000 ARG B 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2164.73 seconds wall clock time: 40 minutes 22.26 seconds (2422.26 seconds total)