Starting phenix.real_space_refine on Sun Sep 13 08:31:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lu1_0977/09_2026/6lu1_0977.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 2 5.49 5 Mg 82 5.21 5 S 80 5.16 5 C 14981 2.51 5 N 2942 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21198 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5819 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 712} Chain: "B" Number of atoms: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5685 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 31, 'TRANS': 681} Chain breaks: 1 Chain: "C" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "D" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1075 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 124} Chain: "E" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 539 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "F" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "I" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 67 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "L" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 994 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "M" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 241 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 2993 Unusual residues: {'BCR': 14, 'CLA': 44, 'LHG': 2, 'PQN': 1} Classifications: {'undetermined': 61} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'CLA:plan-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 10, 'BCR:plan-1': 4, 'BCR:plan-7': 2, 'BCR:plan-8': 3, 'BCR:plan-9': 3, 'BCR:plan-6': 2, 'BCR:plan-2': 2, 'BCR:plan-3': 2, 'BCR:plan-4': 2, 'BCR:plan-5': 1} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 2258 Unusual residues: {'BCR': 6, 'CLA': 35, 'LMG': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 44} Link IDs: {None: 43} Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'CLA:plan-5': 14, 'CLA:plan-4': 6, 'CLA:plan-3': 1, 'BCR:plan-2': 1} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-4': 2, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4440 SG CYS A 578 69.872 48.928 75.101 1.00 9.54 S ATOM 10068 SG CYS B 565 69.435 49.660 82.273 1.00 13.03 S Time building chain proxies: 4.13, per 1000 atoms: 0.19 Number of scatterers: 21198 At special positions: 0 Unit cell: (117.48, 114.81, 153.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 80 16.00 P 2 15.00 Mg 82 11.99 O 3099 8.00 N 2942 7.00 C 14981 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: 2.06 Conformation dependent library (CDL) restraints added in 843.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 804 " pdb="FE4 SF4 B 804 " - pdb=" SG CYS B 565 " pdb="FE3 SF4 B 804 " - pdb=" SG CYS A 578 " pdb="FE2 SF4 B 804 " - pdb=" SG CYS A 587 " pdb="FE1 SF4 B 804 " - pdb=" SG CYS B 574 " pdb=" SF4 C 101 " pdb="FE2 SF4 C 101 " - pdb=" SG CYS C 20 " pdb="FE3 SF4 C 101 " - pdb=" SG CYS C 53 " pdb="FE4 SF4 C 101 " - pdb=" SG CYS C 47 " pdb="FE1 SF4 C 101 " - pdb=" SG CYS C 50 " pdb=" SF4 C 102 " pdb="FE2 SF4 C 102 " - pdb=" SG CYS C 16 " pdb="FE4 SF4 C 102 " - pdb=" SG CYS C 10 " pdb="FE3 SF4 C 102 " - pdb=" SG CYS C 13 " pdb="FE1 SF4 C 102 " - pdb=" SG CYS C 57 " Number of angles added : 36 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 9 sheets defined 54.3% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.598A pdb=" N ALA A 29 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.512A pdb=" N ALA A 39 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG A 40 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 41' Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.938A pdb=" N TRP A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 53 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 54 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 66 through 96 removed outlier: 4.019A pdb=" N PHE A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.747A pdb=" N ILE A 125 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 126 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.644A pdb=" N ARG A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.516A pdb=" N ILE A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.711A pdb=" N PHE A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.752A pdb=" N HIS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 211 through 219 removed outlier: 3.644A pdb=" N HIS A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.646A pdb=" N ASP A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 293 through 312 removed outlier: 3.712A pdb=" N ALA A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.534A pdb=" N LEU A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.506A pdb=" N LEU A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.840A pdb=" N ALA A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 374 removed outlier: 3.563A pdb=" N ILE A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 419 removed outlier: 3.664A pdb=" N PHE A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.866A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 468 removed outlier: 3.643A pdb=" N ILE A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.946A pdb=" N ASN A 492 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 532 through 559 removed outlier: 3.762A pdb=" N HIS A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.908A pdb=" N LEU A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 621 removed outlier: 3.696A pdb=" N VAL A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 608 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.538A pdb=" N ALA A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 652 Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.678A pdb=" N ILE A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 663 " --> pdb=" O SER A 659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 658 through 663' Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.689A pdb=" N GLY A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 680 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.723A pdb=" N SER A 692 " --> pdb=" O MET A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 710 removed outlier: 4.126A pdb=" N TRP A 697 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 755 removed outlier: 3.563A pdb=" N ARG A 728 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 731 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 750 " --> pdb=" O PHE A 746 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 13 removed outlier: 3.602A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.733A pdb=" N TRP B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 48 through 71 removed outlier: 3.863A pdb=" N ILE B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.708A pdb=" N THR B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.624A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.793A pdb=" N TRP B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.764A pdb=" N LEU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.589A pdb=" N LEU B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 221 through 227 removed outlier: 4.234A pdb=" N PHE B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.729A pdb=" N TYR B 232 " --> pdb=" O TRP B 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 233 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.561A pdb=" N ALA B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 removed outlier: 3.695A pdb=" N GLN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 356 removed outlier: 3.501A pdb=" N ALA B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 400 removed outlier: 3.551A pdb=" N MET B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 415 removed outlier: 3.727A pdb=" N LEU B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 448 removed outlier: 3.508A pdb=" N ILE B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 439 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.518A pdb=" N ALA B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.740A pdb=" N ASP B 505 " --> pdb=" O PRO B 501 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 546 removed outlier: 3.614A pdb=" N PHE B 523 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 524 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.800A pdb=" N PHE B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 608 removed outlier: 3.525A pdb=" N TRP B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 606 " --> pdb=" O TRP B 602 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 619 removed outlier: 3.515A pdb=" N ASN B 616 " --> pdb=" O VAL B 612 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 619 " --> pdb=" O PHE B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 628 removed outlier: 3.908A pdb=" N TRP B 625 " --> pdb=" O TYR B 621 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 634 removed outlier: 3.743A pdb=" N SER B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 672 removed outlier: 3.899A pdb=" N LEU B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 664 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 667 " --> pdb=" O TRP B 663 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET B 668 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 690 removed outlier: 4.311A pdb=" N TRP B 677 " --> pdb=" O TRP B 673 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 680 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 737 removed outlier: 3.501A pdb=" N ARG B 712 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 726 " --> pdb=" O GLY B 722 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 727 " --> pdb=" O TYR B 723 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 729 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.645A pdb=" N THR C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'D' and resid 60 through 71 removed outlier: 3.705A pdb=" N CYS D 64 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.694A pdb=" N GLN D 121 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 81 removed outlier: 3.930A pdb=" N LEU F 69 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'I' and resid 10 through 19 Proline residue: I 16 - end of helix Processing helix chain 'I' and resid 21 through 35 removed outlier: 3.883A pdb=" N LEU I 32 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 31 removed outlier: 3.957A pdb=" N ASN J 30 " --> pdb=" O ILE J 27 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG J 31 " --> pdb=" O GLU J 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 27 through 31' Processing helix chain 'L' and resid 9 through 11 No H-bonds generated for 'chain 'L' and resid 9 through 11' Processing helix chain 'L' and resid 24 through 32 removed outlier: 3.539A pdb=" N PHE L 30 " --> pdb=" O LEU L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 55 removed outlier: 3.886A pdb=" N GLY L 47 " --> pdb=" O PRO L 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU L 49 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA L 53 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 64 removed outlier: 3.702A pdb=" N VAL L 63 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 59 through 64' Processing helix chain 'L' and resid 75 through 101 removed outlier: 3.565A pdb=" N SER L 81 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE L 101 " --> pdb=" O GLY L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 135 removed outlier: 3.670A pdb=" N GLN L 119 " --> pdb=" O GLU L 115 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE L 133 " --> pdb=" O MET L 129 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 15 removed outlier: 4.051A pdb=" N VAL M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR M 9 " --> pdb=" O ASP M 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA M 11 " --> pdb=" O GLN M 7 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL M 13 " --> pdb=" O TYR M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 22 Processing helix chain 'M' and resid 22 through 30 removed outlier: 3.613A pdb=" N GLU M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.631A pdb=" N ILE A 137 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 128 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.210A pdb=" N VAL A 520 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AA4, first strand: chain 'C' and resid 64 through 67 removed outlier: 7.894A pdb=" N VAL D 115 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 6 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 26 through 29 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 58 removed outlier: 3.858A pdb=" N ALA D 28 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.826A pdb=" N GLY D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 57 through 60 removed outlier: 6.898A pdb=" N ILE E 37 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 8 " --> pdb=" O GLN E 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.544A pdb=" N LYS L 6 " --> pdb=" O SER L 18 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 9460 1.41 - 1.63: 12448 1.63 - 1.85: 118 1.85 - 2.07: 328 2.07 - 2.28: 36 Bond restraints: 22390 Sorted by residual: bond pdb=" NA CLA L1502 " pdb="MG CLA L1502 " ideal model delta sigma weight residual 2.089 1.944 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" NA CLA L1501 " pdb="MG CLA L1501 " ideal model delta sigma weight residual 2.089 1.948 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" NA CLA B 836 " pdb="MG CLA B 836 " ideal model delta sigma weight residual 2.089 1.948 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" NA CLA B 814 " pdb="MG CLA B 814 " ideal model delta sigma weight residual 2.089 1.950 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" NA CLA A 811 " pdb="MG CLA A 811 " ideal model delta sigma weight residual 2.089 1.950 0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 22385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 30465 4.18 - 8.36: 1089 8.36 - 12.54: 96 12.54 - 16.73: 90 16.73 - 20.91: 2 Bond angle restraints: 31742 Sorted by residual: angle pdb=" C19 BCR F 201 " pdb=" C20 BCR F 201 " pdb=" C21 BCR F 201 " ideal model delta sigma weight residual 122.60 143.51 -20.91 3.00e+00 1.11e-01 4.86e+01 angle pdb=" CBD CLA A 840 " pdb=" CGD CLA A 840 " pdb=" O1D CLA A 840 " ideal model delta sigma weight residual 127.77 110.73 17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" N ILE B 55 " pdb=" CA ILE B 55 " pdb=" C ILE B 55 " ideal model delta sigma weight residual 112.96 107.36 5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" NB CLA A 812 " pdb="MG CLA A 812 " pdb=" ND CLA A 812 " ideal model delta sigma weight residual 176.90 160.79 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" NB CLA B 829 " pdb="MG CLA B 829 " pdb=" ND CLA B 829 " ideal model delta sigma weight residual 176.90 160.84 16.06 3.00e+00 1.11e-01 2.87e+01 ... (remaining 31737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 9337 24.20 - 48.41: 745 48.41 - 72.61: 210 72.61 - 96.82: 53 96.82 - 121.02: 15 Dihedral angle restraints: 10360 sinusoidal: 4725 harmonic: 5635 Sorted by residual: dihedral pdb=" CA TRP B 673 " pdb=" C TRP B 673 " pdb=" N ARG B 674 " pdb=" CA ARG B 674 " ideal model delta harmonic sigma weight residual -180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR B 479 " pdb=" C THR B 479 " pdb=" N LEU B 480 " pdb=" CA LEU B 480 " ideal model delta harmonic sigma weight residual -180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE C 61 " pdb=" C PHE C 61 " pdb=" N LEU C 62 " pdb=" CA LEU C 62 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 10357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2092 0.067 - 0.134: 474 0.134 - 0.201: 100 0.201 - 0.268: 38 0.268 - 0.336: 9 Chirality restraints: 2713 Sorted by residual: chirality pdb=" CB VAL A 713 " pdb=" CA VAL A 713 " pdb=" CG1 VAL A 713 " pdb=" CG2 VAL A 713 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1 LMG B 843 " pdb=" C2 LMG B 843 " pdb=" O1 LMG B 843 " pdb=" O6 LMG B 843 " both_signs ideal model delta sigma weight residual False 2.29 2.62 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C2 LMG B 843 " pdb=" C1 LMG B 843 " pdb=" C3 LMG B 843 " pdb=" O2 LMG B 843 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2710 not shown) Planarity restraints: 4168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CLA L1502 " -0.039 2.00e-02 2.50e+03 2.29e-01 7.83e+02 pdb=" C2A CLA L1502 " -0.330 2.00e-02 2.50e+03 pdb=" C4A CLA L1502 " 0.313 2.00e-02 2.50e+03 pdb=" CHA CLA L1502 " 0.240 2.00e-02 2.50e+03 pdb=" NA CLA L1502 " 0.032 2.00e-02 2.50e+03 pdb="MG CLA L1502 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PQN B 837 " -0.071 2.00e-02 2.50e+03 1.49e-01 7.76e+02 pdb=" C10 PQN B 837 " -0.028 2.00e-02 2.50e+03 pdb=" C11 PQN B 837 " -0.269 2.00e-02 2.50e+03 pdb=" C2 PQN B 837 " 0.090 2.00e-02 2.50e+03 pdb=" C2M PQN B 837 " 0.391 2.00e-02 2.50e+03 pdb=" C3 PQN B 837 " -0.046 2.00e-02 2.50e+03 pdb=" C4 PQN B 837 " 0.011 2.00e-02 2.50e+03 pdb=" C5 PQN B 837 " 0.015 2.00e-02 2.50e+03 pdb=" C6 PQN B 837 " 0.054 2.00e-02 2.50e+03 pdb=" C7 PQN B 837 " 0.058 2.00e-02 2.50e+03 pdb=" C8 PQN B 837 " 0.019 2.00e-02 2.50e+03 pdb=" C9 PQN B 837 " -0.024 2.00e-02 2.50e+03 pdb=" O1 PQN B 837 " -0.245 2.00e-02 2.50e+03 pdb=" O4 PQN B 837 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA B 814 " 0.030 2.00e-02 2.50e+03 2.08e-01 6.51e+02 pdb=" C2A CLA B 814 " 0.302 2.00e-02 2.50e+03 pdb=" C4A CLA B 814 " -0.281 2.00e-02 2.50e+03 pdb=" CHA CLA B 814 " -0.220 2.00e-02 2.50e+03 pdb=" NA CLA B 814 " -0.031 2.00e-02 2.50e+03 pdb="MG CLA B 814 " 0.200 2.00e-02 2.50e+03 ... (remaining 4165 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4133 2.78 - 3.31: 15536 3.31 - 3.84: 33989 3.84 - 4.37: 43319 4.37 - 4.90: 74464 Nonbonded interactions: 171441 Sorted by model distance: nonbonded pdb=" OG SER A 590 " pdb=" OD1 ASP A 593 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 577 " pdb=" OD1 ASP B 580 " model vdw 2.304 3.040 nonbonded pdb=" O SER B 61 " pdb=" OG SER B 61 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR A 280 " pdb=" OG SER A 295 " model vdw 2.311 3.040 nonbonded pdb=" OD2 ASP A 386 " pdb=" OG1 THR A 389 " model vdw 2.314 3.040 ... (remaining 171436 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 individual isotropic 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: 1.120 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 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 : 0.029 0.833 22402 Z= 1.231 Angle : 1.909 38.128 31778 Z= 0.650 Chirality : 0.067 0.336 2713 Planarity : 0.032 0.245 4168 Dihedral : 19.983 121.023 6770 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.98 (0.12), residues: 1964 helix: -4.71 (0.06), residues: 1013 sheet: -2.55 (0.65), residues: 57 loop : -2.99 (0.17), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 129 TYR 0.015 0.002 TYR B 723 PHE 0.022 0.002 PHE A 453 TRP 0.015 0.002 TRP B 59 HIS 0.018 0.002 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.02237 / 1.11 (22390) covalent geometry : angle 1.76547 / 0.65 (31742) hydrogen bonds : bond 0.35557 / 23.71 ( 547) hydrogen bonds : angle 11.01463 / 7.68 ( 1569) metal coordination : bond 0.77523 / 45.35 ( 12) metal coordination : angle 21.64631 / 13.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.642 Fit side-chains REVERT: L 49 GLU cc_start: 0.6884 (tt0) cc_final: 0.6625 (tt0) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1620 time to fit residues: 46.9835 Evaluate side-chains 152 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 61 HIS A 135 HIS A 282 ASN A 286 ASN A 341 HIS A 359 ASN A 373 HIS A 461 HIS A 542 HIS B 13 GLN B 52 HIS B 205 HIS B 322 HIS B 639 ASN C 15 GLN D 54 ASN D 70 GLN D 71 GLN E 18 ASN E 56 ASN L 16 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.128193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.104267 restraints weight = 27224.986| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.10 r_work: 0.2831 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22402 Z= 0.152 Angle : 0.744 28.250 31778 Z= 0.300 Chirality : 0.045 0.309 2713 Planarity : 0.006 0.062 4168 Dihedral : 19.177 109.988 3444 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.00 % Allowed : 8.19 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.15), residues: 1964 helix: -3.17 (0.11), residues: 1047 sheet: -1.85 (0.83), residues: 43 loop : -2.54 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 437 TYR 0.018 0.001 TYR B 599 PHE 0.016 0.001 PHE B 46 TRP 0.012 0.001 TRP A 86 HIS 0.012 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (22390) covalent geometry : angle 0.69259 / 0.30 (31742) hydrogen bonds : bond 0.06822 / 4.54 ( 547) hydrogen bonds : angle 5.16679 / 3.51 ( 1569) metal coordination : bond 0.01662 / 0.98 ( 12) metal coordination : angle 8.06775 / 5.35 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.570 Fit side-chains REVERT: B 205 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7320 (t-90) REVERT: D 53 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: D 80 TYR cc_start: 0.8928 (p90) cc_final: 0.8695 (p90) REVERT: E 39 ARG cc_start: 0.7636 (tmm160) cc_final: 0.7405 (tmm160) outliers start: 16 outliers final: 13 residues processed: 177 average time/residue: 0.1529 time to fit residues: 42.6150 Evaluate side-chains 163 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain L residue 16 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 GLN C 15 GLN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.125469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.101314 restraints weight = 27439.877| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.08 r_work: 0.2789 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22402 Z= 0.203 Angle : 0.770 26.434 31778 Z= 0.309 Chirality : 0.046 0.263 2713 Planarity : 0.006 0.060 4168 Dihedral : 17.938 109.633 3444 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.25 % Allowed : 10.44 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.16), residues: 1964 helix: -2.19 (0.14), residues: 1042 sheet: -1.81 (0.80), residues: 49 loop : -2.35 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 43 TYR 0.016 0.001 TYR B 599 PHE 0.017 0.002 PHE A 394 TRP 0.013 0.001 TRP A 86 HIS 0.016 0.001 HIS L 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (22390) covalent geometry : angle 0.72145 / 0.31 (31742) hydrogen bonds : bond 0.06580 / 4.39 ( 547) hydrogen bonds : angle 4.76645 / 3.23 ( 1569) metal coordination : bond 0.00948 / 0.46 ( 12) metal coordination : angle 8.06703 / 5.40 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.623 Fit side-chains REVERT: A 424 MET cc_start: 0.7414 (ttm) cc_final: 0.7008 (ttp) REVERT: D 80 TYR cc_start: 0.8998 (p90) cc_final: 0.8743 (p90) REVERT: E 39 ARG cc_start: 0.7801 (tmm160) cc_final: 0.7575 (tmm160) outliers start: 20 outliers final: 17 residues processed: 168 average time/residue: 0.1550 time to fit residues: 41.1984 Evaluate side-chains 164 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 135 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 187 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 15 GLN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.102723 restraints weight = 27251.713| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.13 r_work: 0.2800 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22402 Z= 0.144 Angle : 0.686 26.730 31778 Z= 0.273 Chirality : 0.043 0.234 2713 Planarity : 0.005 0.055 4168 Dihedral : 17.097 109.220 3444 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.38 % Allowed : 11.88 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.17), residues: 1964 helix: -1.58 (0.15), residues: 1035 sheet: -1.49 (0.84), residues: 49 loop : -2.15 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 43 TYR 0.012 0.001 TYR B 599 PHE 0.015 0.001 PHE A 394 TRP 0.012 0.001 TRP A 86 HIS 0.006 0.001 HIS B 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (22390) covalent geometry : angle 0.63386 / 0.27 (31742) hydrogen bonds : bond 0.05388 / 3.59 ( 547) hydrogen bonds : angle 4.43243 / 2.99 ( 1569) metal coordination : bond 0.00756 / 0.38 ( 12) metal coordination : angle 7.81778 / 5.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.620 Fit side-chains REVERT: A 424 MET cc_start: 0.7108 (ttm) cc_final: 0.6735 (ttp) REVERT: E 39 ARG cc_start: 0.7660 (tmm160) cc_final: 0.7458 (tmm160) outliers start: 22 outliers final: 16 residues processed: 177 average time/residue: 0.1566 time to fit residues: 43.8122 Evaluate side-chains 172 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain M residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.2980 chunk 50 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 168 optimal weight: 30.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 205 HIS C 15 GLN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.127736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103490 restraints weight = 27157.514| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.10 r_work: 0.2826 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22402 Z= 0.127 Angle : 0.650 23.591 31778 Z= 0.260 Chirality : 0.042 0.218 2713 Planarity : 0.004 0.054 4168 Dihedral : 16.480 108.778 3444 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.44 % Allowed : 12.88 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.18), residues: 1964 helix: -1.16 (0.15), residues: 1038 sheet: -1.28 (0.85), residues: 49 loop : -2.01 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.011 0.001 TYR B 599 PHE 0.013 0.001 PHE A 394 TRP 0.011 0.001 TRP A 697 HIS 0.006 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22390) covalent geometry : angle 0.60308 / 0.26 (31742) hydrogen bonds : bond 0.04976 / 3.32 ( 547) hydrogen bonds : angle 4.25730 / 2.87 ( 1569) metal coordination : bond 0.00644 / 0.33 ( 12) metal coordination : angle 7.24108 / 4.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.640 Fit side-chains REVERT: B 205 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7554 (t-90) outliers start: 23 outliers final: 18 residues processed: 179 average time/residue: 0.1595 time to fit residues: 44.9908 Evaluate side-chains 174 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain M residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 30 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 chunk 161 optimal weight: 30.0000 chunk 135 optimal weight: 5.9990 chunk 191 optimal weight: 0.8980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 HIS E 56 ASN ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.100698 restraints weight = 27209.124| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.10 r_work: 0.2766 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22402 Z= 0.201 Angle : 0.738 26.275 31778 Z= 0.296 Chirality : 0.046 0.256 2713 Planarity : 0.005 0.053 4168 Dihedral : 16.723 109.027 3444 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.75 % Allowed : 13.32 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.18), residues: 1964 helix: -1.17 (0.15), residues: 1037 sheet: -1.18 (0.75), residues: 61 loop : -1.97 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 43 TYR 0.014 0.001 TYR B 599 PHE 0.017 0.002 PHE A 267 TRP 0.012 0.001 TRP A 86 HIS 0.018 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (22390) covalent geometry : angle 0.68849 / 0.30 (31742) hydrogen bonds : bond 0.05969 / 3.98 ( 547) hydrogen bonds : angle 4.42790 / 2.99 ( 1569) metal coordination : bond 0.01107 / 0.57 ( 12) metal coordination : angle 7.92547 / 5.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.611 Fit side-chains REVERT: A 424 MET cc_start: 0.7163 (ttm) cc_final: 0.6794 (ttp) REVERT: M 3 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7280 (mp) outliers start: 28 outliers final: 25 residues processed: 178 average time/residue: 0.1514 time to fit residues: 42.9810 Evaluate side-chains 183 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 20 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.102612 restraints weight = 27098.185| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.10 r_work: 0.2813 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22402 Z= 0.136 Angle : 0.664 25.785 31778 Z= 0.265 Chirality : 0.043 0.220 2713 Planarity : 0.004 0.051 4168 Dihedral : 16.463 107.727 3444 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.44 % Allowed : 14.26 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 1964 helix: -0.91 (0.16), residues: 1038 sheet: -1.22 (0.85), residues: 49 loop : -1.88 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 43 TYR 0.011 0.001 TYR B 599 PHE 0.018 0.001 PHE A 267 TRP 0.012 0.001 TRP A 86 HIS 0.006 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (22390) covalent geometry : angle 0.61249 / 0.26 (31742) hydrogen bonds : bond 0.05144 / 3.43 ( 547) hydrogen bonds : angle 4.27890 / 2.88 ( 1569) metal coordination : bond 0.00698 / 0.34 ( 12) metal coordination : angle 7.67318 / 5.17 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.637 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 178 average time/residue: 0.1503 time to fit residues: 42.4451 Evaluate side-chains 177 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain M residue 20 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 147 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 120 optimal weight: 8.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.130491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.106807 restraints weight = 26950.741| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.12 r_work: 0.2846 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22402 Z= 0.087 Angle : 0.579 20.966 31778 Z= 0.233 Chirality : 0.040 0.177 2713 Planarity : 0.004 0.048 4168 Dihedral : 15.742 99.190 3444 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.19 % Allowed : 14.38 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.18), residues: 1964 helix: -0.51 (0.16), residues: 1039 sheet: -1.18 (0.76), residues: 59 loop : -1.73 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.009 0.001 TYR B 356 PHE 0.017 0.001 PHE A 267 TRP 0.011 0.001 TRP A 86 HIS 0.005 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (22390) covalent geometry : angle 0.53376 / 0.23 (31742) hydrogen bonds : bond 0.03910 / 2.60 ( 547) hydrogen bonds : angle 4.00769 / 2.69 ( 1569) metal coordination : bond 0.00488 / 0.31 ( 12) metal coordination : angle 6.70842 / 4.46 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.641 Fit side-chains REVERT: B 3 LYS cc_start: 0.7632 (pttm) cc_final: 0.6707 (tppt) REVERT: B 386 MET cc_start: 0.9304 (mmm) cc_final: 0.9079 (mmt) outliers start: 19 outliers final: 14 residues processed: 188 average time/residue: 0.1496 time to fit residues: 44.5915 Evaluate side-chains 174 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 92 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN B 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.123679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.099421 restraints weight = 27271.600| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.07 r_work: 0.2756 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22402 Z= 0.271 Angle : 0.820 28.130 31778 Z= 0.328 Chirality : 0.050 0.304 2713 Planarity : 0.005 0.050 4168 Dihedral : 16.727 88.089 3444 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.75 % Allowed : 14.26 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 1964 helix: -0.94 (0.15), residues: 1038 sheet: -1.12 (0.74), residues: 63 loop : -1.84 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 43 TYR 0.016 0.002 TYR B 599 PHE 0.019 0.002 PHE A 544 TRP 0.015 0.002 TRP B 663 HIS 0.011 0.002 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.27 (22390) covalent geometry : angle 0.76590 / 0.33 (31742) hydrogen bonds : bond 0.06614 / 4.40 ( 547) hydrogen bonds : angle 4.51060 / 3.05 ( 1569) metal coordination : bond 0.01377 / 0.68 ( 12) metal coordination : angle 8.71648 / 5.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.678 Fit side-chains REVERT: A 424 MET cc_start: 0.7361 (ttm) cc_final: 0.6936 (ttp) REVERT: B 611 ASN cc_start: 0.8137 (t0) cc_final: 0.7917 (t0) REVERT: M 3 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7445 (mp) outliers start: 28 outliers final: 24 residues processed: 176 average time/residue: 0.1501 time to fit residues: 41.8999 Evaluate side-chains 180 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain M residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.103133 restraints weight = 27279.024| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.09 r_work: 0.2802 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22402 Z= 0.125 Angle : 0.656 25.811 31778 Z= 0.262 Chirality : 0.042 0.210 2713 Planarity : 0.004 0.049 4168 Dihedral : 16.029 82.636 3444 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.25 % Allowed : 14.88 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.18), residues: 1964 helix: -0.61 (0.16), residues: 1041 sheet: -1.15 (0.86), residues: 49 loop : -1.77 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 24 TYR 0.009 0.001 TYR B 599 PHE 0.016 0.001 PHE B 644 TRP 0.012 0.001 TRP A 86 HIS 0.006 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22390) covalent geometry : angle 0.60302 / 0.26 (31742) hydrogen bonds : bond 0.04870 / 3.25 ( 547) hydrogen bonds : angle 4.22764 / 2.84 ( 1569) metal coordination : bond 0.00584 / 0.28 ( 12) metal coordination : angle 7.71740 / 5.24 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.637 Fit side-chains REVERT: B 386 MET cc_start: 0.9316 (mmm) cc_final: 0.8999 (mmt) REVERT: M 3 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7220 (mp) outliers start: 20 outliers final: 18 residues processed: 177 average time/residue: 0.1555 time to fit residues: 43.6408 Evaluate side-chains 177 residues out of total 1599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain M residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 66 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.103235 restraints weight = 27080.473| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.10 r_work: 0.2816 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22402 Z= 0.130 Angle : 0.649 23.818 31778 Z= 0.262 Chirality : 0.042 0.206 2713 Planarity : 0.004 0.048 4168 Dihedral : 15.875 82.095 3444 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.19 % Allowed : 15.20 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.18), residues: 1964 helix: -0.50 (0.16), residues: 1040 sheet: -1.13 (0.86), residues: 49 loop : -1.71 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 43 TYR 0.010 0.001 TYR B 599 PHE 0.015 0.001 PHE B 644 TRP 0.011 0.001 TRP A 86 HIS 0.006 0.001 HIS A 461 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22390) covalent geometry : angle 0.60014 / 0.26 (31742) hydrogen bonds : bond 0.04914 / 3.28 ( 547) hydrogen bonds : angle 4.19274 / 2.81 ( 1569) metal coordination : bond 0.00668 / 0.32 ( 12) metal coordination : angle 7.38852 / 4.90 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.30 seconds wall clock time: 71 minutes 15.31 seconds (4275.31 seconds total)