Starting phenix.real_space_refine on Tue Aug 26 02:49:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bkg_16097/08_2025/8bkg_16097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bkg_16097/08_2025/8bkg_16097.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/8bkg_16097/08_2025/8bkg_16097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bkg_16097/08_2025/8bkg_16097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bkg_16097/08_2025/8bkg_16097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bkg_16097/08_2025/8bkg_16097.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= 0.001 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 20760 2.51 5 N 5808 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32824 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 58, 'TRANS': 958} Restraints were copied for chains: B, C, D Time building chain proxies: 8.93, per 1000 atoms: 0.27 Number of scatterers: 32824 At special positions: 0 Unit cell: (194.79, 152.51, 104.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 6100 8.00 N 5808 7.00 C 20760 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: 2.28 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 52 sheets defined 17.9% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 13 " --> pdb=" O VAL A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 465 through 479 Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY A 490 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP A 492 " --> pdb=" O GLY A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN A1008 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY B 490 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 492 " --> pdb=" O GLY B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 813 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN B1008 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 13 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY C 490 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP C 492 " --> pdb=" O GLY C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 13 removed outlier: 3.584A pdb=" N VAL D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.790A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.745A pdb=" N HIS D 93 " --> pdb=" O ASN D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 removed outlier: 4.007A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.809A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 440 through 447 Processing helix chain 'D' and resid 465 through 479 Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.565A pdb=" N GLY D 490 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 491 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP D 492 " --> pdb=" O GLY D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 487 through 492' Processing helix chain 'D' and resid 519 through 525 Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 599 through 603 removed outlier: 3.860A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.136A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 813 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.736A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.523A pdb=" N GLN D1008 " --> pdb=" O ALA D1005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP A 568 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU A 537 " --> pdb=" O TRP A 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP B 568 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU B 537 " --> pdb=" O TRP B 568 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD1, first strand: chain 'C' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP C 568 " --> pdb=" O LEU C 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU C 537 " --> pdb=" O TRP C 568 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE5, first strand: chain 'D' and resid 82 through 86 removed outlier: 8.773A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.168A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.662A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.873A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 7.910A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N TRP D 568 " --> pdb=" O LEU D 535 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N GLU D 537 " --> pdb=" O TRP D 568 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 5.866A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.139A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.334A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.452A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.547A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.352A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 7.029A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3144 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: 7.46 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11072 1.34 - 1.46: 8220 1.46 - 1.58: 14252 1.58 - 1.70: 0 1.70 - 1.82: 248 Bond restraints: 33792 Sorted by residual: bond pdb=" C THR C 595 " pdb=" N PRO C 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" C THR D 595 " pdb=" N PRO D 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" C THR B 595 " pdb=" N PRO B 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" C THR A 595 " pdb=" N PRO A 596 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.04e+00 bond pdb=" CA ASN C 958 " pdb=" CB ASN C 958 " ideal model delta sigma weight residual 1.534 1.556 -0.023 1.72e-02 3.38e+03 1.74e+00 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 45656 2.47 - 4.94: 424 4.94 - 7.41: 12 7.41 - 9.87: 8 9.87 - 12.34: 4 Bond angle restraints: 46104 Sorted by residual: angle pdb=" N GLY A 488 " pdb=" CA GLY A 488 " pdb=" C GLY A 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLY D 488 " pdb=" CA GLY D 488 " pdb=" C GLY D 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLY B 488 " pdb=" CA GLY B 488 " pdb=" C GLY B 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" N GLY C 488 " pdb=" CA GLY C 488 " pdb=" C GLY C 488 " ideal model delta sigma weight residual 111.36 116.19 -4.83 1.17e+00 7.31e-01 1.70e+01 angle pdb=" CB MET D 745 " pdb=" CG MET D 745 " pdb=" SD MET D 745 " ideal model delta sigma weight residual 112.70 125.04 -12.34 3.00e+00 1.11e-01 1.69e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 17424 17.20 - 34.40: 1800 34.40 - 51.60: 432 51.60 - 68.81: 100 68.81 - 86.01: 44 Dihedral angle restraints: 19800 sinusoidal: 7984 harmonic: 11816 Sorted by residual: dihedral pdb=" CA GLU B 580 " pdb=" C GLU B 580 " pdb=" N ASN B 581 " pdb=" CA ASN B 581 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU D 580 " pdb=" C GLU D 580 " pdb=" N ASN D 581 " pdb=" CA ASN D 581 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU A 580 " pdb=" C GLU A 580 " pdb=" N ASN A 581 " pdb=" CA ASN A 581 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 19797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3252 0.037 - 0.073: 1100 0.073 - 0.110: 348 0.110 - 0.147: 112 0.147 - 0.183: 8 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CA THR C 595 " pdb=" N THR C 595 " pdb=" C THR C 595 " pdb=" CB THR C 595 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA THR A 595 " pdb=" N THR A 595 " pdb=" C THR A 595 " pdb=" CB THR A 595 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA THR D 595 " pdb=" N THR D 595 " pdb=" C THR D 595 " pdb=" CB THR D 595 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 ... (remaining 4817 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 906 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO C 907 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 907 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 907 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 906 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 907 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 907 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 907 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 906 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO D 907 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 907 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 907 " 0.027 5.00e-02 4.00e+02 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5438 2.77 - 3.30: 28330 3.30 - 3.84: 57982 3.84 - 4.37: 69062 4.37 - 4.90: 120642 Nonbonded interactions: 281454 Sorted by model distance: nonbonded pdb=" O ASP A 594 " pdb=" ND2 ASN A 597 " model vdw 2.241 3.120 nonbonded pdb=" O ASP D 594 " pdb=" ND2 ASN D 597 " model vdw 2.241 3.120 nonbonded pdb=" O ASP C 594 " pdb=" ND2 ASN C 597 " model vdw 2.241 3.120 nonbonded pdb=" O ASP B 594 " pdb=" ND2 ASN B 597 " model vdw 2.241 3.120 nonbonded pdb=" O PRO D 434 " pdb=" OG SER D 437 " model vdw 2.248 3.040 ... (remaining 281449 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.350 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.490 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.003 0.049 33792 Z= 0.130 Angle : 0.572 12.342 46104 Z= 0.310 Chirality : 0.043 0.183 4820 Planarity : 0.004 0.049 6088 Dihedral : 15.302 86.007 12192 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.57 % Allowed : 16.36 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.35 (0.13), residues: 4080 helix: -0.76 (0.21), residues: 540 sheet: 0.47 (0.14), residues: 1352 loop : -0.48 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 894 TYR 0.014 0.001 TYR B1016 PHE 0.007 0.001 PHE A 274 TRP 0.018 0.001 TRP B 90 HIS 0.009 0.001 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.00281 (33792) covalent geometry : angle 0.57231 (46104) hydrogen bonds : bond 0.15241 ( 1132) hydrogen bonds : angle 6.25286 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.279 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 228 average time/residue: 0.1989 time to fit residues: 74.0007 Evaluate side-chains 220 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 837 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 93 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 38 ASN B 93 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 38 ASN C 93 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 38 ASN D 93 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.088639 restraints weight = 55814.964| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.62 r_work: 0.2997 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33792 Z= 0.235 Angle : 0.585 9.249 46104 Z= 0.305 Chirality : 0.047 0.160 4820 Planarity : 0.005 0.045 6088 Dihedral : 4.939 41.499 4496 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.17 % Allowed : 13.84 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.25 (0.13), residues: 4080 helix: -0.34 (0.22), residues: 524 sheet: 0.24 (0.14), residues: 1460 loop : -0.32 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 356 TYR 0.015 0.002 TYR D 486 PHE 0.013 0.002 PHE C 143 TRP 0.015 0.002 TRP A 90 HIS 0.006 0.001 HIS B 653 Details of bonding type rmsd covalent geometry : bond 0.00549 (33792) covalent geometry : angle 0.58489 (46104) hydrogen bonds : bond 0.03593 ( 1132) hydrogen bonds : angle 4.84242 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 1.315 Fit side-chains REVERT: A 92 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7822 (mmm) REVERT: A 103 VAL cc_start: 0.8740 (t) cc_final: 0.8528 (m) REVERT: A 226 HIS cc_start: 0.7392 (m170) cc_final: 0.7188 (m170) REVERT: A 671 ASP cc_start: 0.8183 (t0) cc_final: 0.7872 (t0) REVERT: A 910 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 92 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7824 (mmm) REVERT: B 103 VAL cc_start: 0.8727 (t) cc_final: 0.8517 (m) REVERT: B 226 HIS cc_start: 0.7411 (m170) cc_final: 0.7206 (m170) REVERT: B 671 ASP cc_start: 0.8183 (t0) cc_final: 0.7872 (t0) REVERT: B 910 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8499 (pp) REVERT: C 92 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: C 103 VAL cc_start: 0.8743 (t) cc_final: 0.8532 (m) REVERT: C 226 HIS cc_start: 0.7416 (m170) cc_final: 0.7213 (m170) REVERT: C 671 ASP cc_start: 0.8174 (t0) cc_final: 0.7864 (t0) REVERT: C 910 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8504 (pp) REVERT: D 92 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.7850 (mmm) REVERT: D 103 VAL cc_start: 0.8730 (t) cc_final: 0.8521 (m) REVERT: D 226 HIS cc_start: 0.7406 (m170) cc_final: 0.7202 (m170) REVERT: D 671 ASP cc_start: 0.8149 (t0) cc_final: 0.7836 (t0) REVERT: D 910 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8496 (pp) outliers start: 76 outliers final: 36 residues processed: 296 average time/residue: 0.2420 time to fit residues: 114.1968 Evaluate side-chains 260 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 234 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 366 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 377 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087500 restraints weight = 55633.548| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.62 r_work: 0.2971 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33792 Z= 0.196 Angle : 0.534 9.582 46104 Z= 0.277 Chirality : 0.045 0.155 4820 Planarity : 0.004 0.043 6088 Dihedral : 4.686 36.535 4488 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.03 % Allowed : 14.56 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.14 (0.13), residues: 4080 helix: 0.01 (0.23), residues: 524 sheet: 0.27 (0.14), residues: 1472 loop : -0.27 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 909 TYR 0.013 0.002 TYR D 588 PHE 0.009 0.001 PHE D 225 TRP 0.020 0.002 TRP A 90 HIS 0.004 0.001 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00458 (33792) covalent geometry : angle 0.53377 (46104) hydrogen bonds : bond 0.03455 ( 1132) hydrogen bonds : angle 4.74473 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 1.370 Fit side-chains REVERT: A 92 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7745 (mmm) REVERT: A 438 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: A 910 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8548 (pp) REVERT: B 438 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: B 910 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 92 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7790 (mmm) REVERT: C 438 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: C 910 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8554 (pp) REVERT: D 92 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7767 (mmm) REVERT: D 438 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: D 910 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8548 (pp) outliers start: 71 outliers final: 36 residues processed: 280 average time/residue: 0.2235 time to fit residues: 103.0915 Evaluate side-chains 247 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 11 optimal weight: 4.9990 chunk 311 optimal weight: 1.9990 chunk 367 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 chunk 237 optimal weight: 0.0370 chunk 268 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 317 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 298 optimal weight: 0.7980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 135 GLN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 135 GLN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 135 GLN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 905 ASN ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.090191 restraints weight = 54922.534| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.61 r_work: 0.3011 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 33792 Z= 0.091 Angle : 0.453 9.071 46104 Z= 0.237 Chirality : 0.042 0.140 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.264 31.600 4484 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.17 % Allowed : 14.36 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: 0.10 (0.13), residues: 4080 helix: 0.47 (0.23), residues: 524 sheet: 0.40 (0.14), residues: 1460 loop : -0.18 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 439 TYR 0.010 0.001 TYR A 906 PHE 0.006 0.001 PHE A 63 TRP 0.017 0.001 TRP A 553 HIS 0.002 0.000 HIS D 391 Details of bonding type rmsd covalent geometry : bond 0.00212 (33792) covalent geometry : angle 0.45308 (46104) hydrogen bonds : bond 0.02557 ( 1132) hydrogen bonds : angle 4.44498 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 228 time to evaluate : 1.484 Fit side-chains REVERT: A 92 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7887 (mmp) REVERT: A 910 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8523 (pp) REVERT: B 92 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7876 (mmp) REVERT: B 910 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8531 (pp) REVERT: C 92 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7879 (mmp) REVERT: C 910 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8531 (pp) REVERT: D 92 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7905 (mmp) REVERT: D 910 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8522 (pp) outliers start: 76 outliers final: 28 residues processed: 284 average time/residue: 0.2264 time to fit residues: 106.3694 Evaluate side-chains 236 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 254 optimal weight: 0.2980 chunk 345 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 371 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 252 optimal weight: 0.6980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 38 ASN B 135 GLN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN C 38 ASN C 135 GLN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 ASN D 38 ASN D 135 GLN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.100647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088721 restraints weight = 55278.108| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.61 r_work: 0.2991 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33792 Z= 0.136 Angle : 0.479 9.349 46104 Z= 0.248 Chirality : 0.043 0.149 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.324 32.117 4484 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.32 % Allowed : 14.36 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: 0.11 (0.13), residues: 4080 helix: 0.56 (0.24), residues: 524 sheet: 0.39 (0.14), residues: 1472 loop : -0.18 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 599 TYR 0.011 0.001 TYR A 906 PHE 0.007 0.001 PHE C 143 TRP 0.016 0.001 TRP A 90 HIS 0.003 0.001 HIS C 653 Details of bonding type rmsd covalent geometry : bond 0.00323 (33792) covalent geometry : angle 0.47910 (46104) hydrogen bonds : bond 0.02773 ( 1132) hydrogen bonds : angle 4.49036 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 208 time to evaluate : 1.491 Fit side-chains REVERT: A 92 MET cc_start: 0.8507 (mmm) cc_final: 0.7914 (mmp) REVERT: A 438 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: A 906 TYR cc_start: 0.8901 (m-80) cc_final: 0.8293 (m-80) REVERT: A 910 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8528 (pp) REVERT: A 958 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7692 (p0) REVERT: B 92 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7922 (mmp) REVERT: B 438 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: B 906 TYR cc_start: 0.8909 (m-80) cc_final: 0.8293 (m-80) REVERT: B 910 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8534 (pp) REVERT: B 958 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7697 (p0) REVERT: C 92 MET cc_start: 0.8509 (mmm) cc_final: 0.7913 (mmp) REVERT: C 438 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: C 906 TYR cc_start: 0.8917 (m-80) cc_final: 0.8304 (m-80) REVERT: C 910 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8537 (pp) REVERT: C 958 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7697 (p0) REVERT: D 92 MET cc_start: 0.8522 (mmm) cc_final: 0.7943 (mmp) REVERT: D 438 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: D 906 TYR cc_start: 0.8906 (m-80) cc_final: 0.8293 (m-80) REVERT: D 910 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8530 (pp) REVERT: D 958 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7698 (p0) outliers start: 81 outliers final: 43 residues processed: 280 average time/residue: 0.2240 time to fit residues: 103.6273 Evaluate side-chains 256 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 63 optimal weight: 8.9990 chunk 378 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN A1022 GLN B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN B1022 GLN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 ASN C1022 GLN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN D1022 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.086217 restraints weight = 55647.500| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.61 r_work: 0.2951 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 33792 Z= 0.233 Angle : 0.548 9.624 46104 Z= 0.284 Chirality : 0.046 0.161 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.618 33.587 4484 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 2.20 % Allowed : 14.62 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.03 (0.13), residues: 4080 helix: 0.37 (0.23), residues: 524 sheet: 0.33 (0.14), residues: 1472 loop : -0.28 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 909 TYR 0.015 0.002 TYR C 588 PHE 0.011 0.001 PHE C 143 TRP 0.019 0.002 TRP D 90 HIS 0.005 0.001 HIS C1015 Details of bonding type rmsd covalent geometry : bond 0.00549 (33792) covalent geometry : angle 0.54779 (46104) hydrogen bonds : bond 0.03330 ( 1132) hydrogen bonds : angle 4.68544 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 211 time to evaluate : 1.424 Fit side-chains REVERT: A 40 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: A 92 MET cc_start: 0.8489 (mmm) cc_final: 0.7855 (mmp) REVERT: A 906 TYR cc_start: 0.8818 (m-80) cc_final: 0.8270 (m-80) REVERT: A 910 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 958 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7752 (p0) REVERT: A 984 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 40 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: B 92 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7781 (mmp) REVERT: B 906 TYR cc_start: 0.8824 (m-80) cc_final: 0.8272 (m-80) REVERT: B 910 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8592 (pp) REVERT: B 958 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7751 (p0) REVERT: B 984 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8669 (tp) REVERT: C 40 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: C 92 MET cc_start: 0.8491 (mmm) cc_final: 0.7853 (mmp) REVERT: C 906 TYR cc_start: 0.8831 (m-80) cc_final: 0.8278 (m-80) REVERT: C 910 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8633 (pp) REVERT: C 958 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.7755 (p0) REVERT: C 984 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8666 (tp) REVERT: D 40 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: D 92 MET cc_start: 0.8513 (mmm) cc_final: 0.7891 (mmp) REVERT: D 906 TYR cc_start: 0.8821 (m-80) cc_final: 0.8268 (m-80) REVERT: D 910 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8624 (pp) REVERT: D 958 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7754 (p0) REVERT: D 984 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8654 (tp) outliers start: 77 outliers final: 40 residues processed: 279 average time/residue: 0.2299 time to fit residues: 105.7314 Evaluate side-chains 258 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 984 LEU Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 253 optimal weight: 4.9990 chunk 378 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN B 958 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 958 ASN D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN D 958 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.098620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.086738 restraints weight = 55667.554| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.61 r_work: 0.2953 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33792 Z= 0.170 Angle : 0.511 9.478 46104 Z= 0.265 Chirality : 0.044 0.160 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.559 32.787 4484 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Rotamer: Outliers : 2.15 % Allowed : 14.93 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.05 (0.13), residues: 4080 helix: 0.41 (0.23), residues: 524 sheet: 0.30 (0.14), residues: 1472 loop : -0.30 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 909 TYR 0.012 0.002 TYR D 123 PHE 0.008 0.001 PHE B 143 TRP 0.019 0.001 TRP D 90 HIS 0.003 0.001 HIS B1015 Details of bonding type rmsd covalent geometry : bond 0.00399 (33792) covalent geometry : angle 0.51052 (46104) hydrogen bonds : bond 0.03070 ( 1132) hydrogen bonds : angle 4.65927 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 1.338 Fit side-chains REVERT: A 40 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: A 92 MET cc_start: 0.8494 (mmm) cc_final: 0.7877 (mmp) REVERT: A 438 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 906 TYR cc_start: 0.8822 (m-80) cc_final: 0.8260 (m-80) REVERT: A 910 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 958 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7837 (p0) REVERT: B 40 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: B 92 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7920 (mmp) REVERT: B 438 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: B 906 TYR cc_start: 0.8881 (m-80) cc_final: 0.8276 (m-80) REVERT: B 910 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8600 (pp) REVERT: B 958 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.7848 (p0) REVERT: C 40 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: C 92 MET cc_start: 0.8503 (mmm) cc_final: 0.7882 (mmp) REVERT: C 438 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: C 906 TYR cc_start: 0.8884 (m-80) cc_final: 0.8276 (m-80) REVERT: C 910 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8604 (pp) REVERT: C 958 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7851 (p0) REVERT: D 40 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: D 92 MET cc_start: 0.8524 (mmm) cc_final: 0.7928 (mmp) REVERT: D 438 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: D 906 TYR cc_start: 0.8875 (m-80) cc_final: 0.8265 (m-80) REVERT: D 910 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8629 (pp) REVERT: D 958 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7851 (p0) outliers start: 75 outliers final: 39 residues processed: 279 average time/residue: 0.2326 time to fit residues: 106.6370 Evaluate side-chains 260 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 610 ASP Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 331 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 406 optimal weight: 0.3980 chunk 155 optimal weight: 9.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A 958 ASN B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN B 958 ASN C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 958 ASN D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN D 958 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.087940 restraints weight = 55449.454| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.61 r_work: 0.2971 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33792 Z= 0.112 Angle : 0.477 9.218 46104 Z= 0.248 Chirality : 0.043 0.159 4820 Planarity : 0.004 0.039 6088 Dihedral : 4.391 30.169 4484 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.89 % Allowed : 14.99 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: 0.04 (0.13), residues: 4080 helix: 0.56 (0.24), residues: 524 sheet: 0.35 (0.14), residues: 1464 loop : -0.26 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 909 TYR 0.012 0.001 TYR A1016 PHE 0.006 0.001 PHE C 150 TRP 0.018 0.001 TRP A 553 HIS 0.003 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00264 (33792) covalent geometry : angle 0.47656 (46104) hydrogen bonds : bond 0.02787 ( 1132) hydrogen bonds : angle 4.54141 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 1.380 Fit side-chains REVERT: A 92 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7919 (mmp) REVERT: A 438 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 906 TYR cc_start: 0.8865 (m-80) cc_final: 0.8253 (m-80) REVERT: A 910 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8610 (pp) REVERT: A 958 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7734 (p0) REVERT: B 92 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7931 (mmp) REVERT: B 906 TYR cc_start: 0.8874 (m-80) cc_final: 0.8254 (m-80) REVERT: B 910 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8627 (pp) REVERT: B 958 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.7730 (p0) REVERT: C 92 MET cc_start: 0.8494 (mmm) cc_final: 0.7906 (mmp) REVERT: C 438 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: C 906 TYR cc_start: 0.8879 (m-80) cc_final: 0.8264 (m-80) REVERT: C 910 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8629 (pp) REVERT: C 958 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7737 (p0) REVERT: D 92 MET cc_start: 0.8514 (mmm) cc_final: 0.7944 (mmp) REVERT: D 438 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: D 906 TYR cc_start: 0.8874 (m-80) cc_final: 0.8254 (m-80) REVERT: D 910 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8614 (pp) REVERT: D 958 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7736 (p0) outliers start: 66 outliers final: 32 residues processed: 264 average time/residue: 0.2132 time to fit residues: 92.2730 Evaluate side-chains 245 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 438 GLU Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 269 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.086672 restraints weight = 55492.176| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.60 r_work: 0.2952 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33792 Z= 0.180 Angle : 0.514 9.415 46104 Z= 0.266 Chirality : 0.045 0.157 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.527 32.227 4484 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 1.66 % Allowed : 15.05 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.07 (0.13), residues: 4080 helix: 0.47 (0.24), residues: 524 sheet: 0.28 (0.14), residues: 1472 loop : -0.33 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 909 TYR 0.013 0.002 TYR B1016 PHE 0.009 0.001 PHE A 143 TRP 0.017 0.001 TRP C 90 HIS 0.004 0.001 HIS C1015 Details of bonding type rmsd covalent geometry : bond 0.00425 (33792) covalent geometry : angle 0.51377 (46104) hydrogen bonds : bond 0.03055 ( 1132) hydrogen bonds : angle 4.63643 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 1.168 Fit side-chains REVERT: A 40 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: A 92 MET cc_start: 0.8505 (mmm) cc_final: 0.7909 (mmp) REVERT: A 906 TYR cc_start: 0.8888 (m-80) cc_final: 0.8278 (m-80) REVERT: A 910 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8644 (pp) REVERT: A 958 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7721 (p0) REVERT: B 40 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: B 92 MET cc_start: 0.8518 (mmm) cc_final: 0.7942 (mmp) REVERT: B 438 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: B 906 TYR cc_start: 0.8905 (m-80) cc_final: 0.8291 (m-80) REVERT: B 910 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8662 (pp) REVERT: B 958 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7719 (p0) REVERT: C 40 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: C 92 MET cc_start: 0.8496 (mmm) cc_final: 0.7892 (mmp) REVERT: C 906 TYR cc_start: 0.8904 (m-80) cc_final: 0.8292 (m-80) REVERT: C 910 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8663 (pp) REVERT: C 958 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7723 (p0) REVERT: D 40 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: D 92 MET cc_start: 0.8519 (mmm) cc_final: 0.7936 (mmp) REVERT: D 906 TYR cc_start: 0.8901 (m-80) cc_final: 0.8284 (m-80) REVERT: D 910 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8652 (pp) REVERT: D 958 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7721 (p0) outliers start: 58 outliers final: 34 residues processed: 248 average time/residue: 0.2126 time to fit residues: 86.0164 Evaluate side-chains 243 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 0.0000 chunk 207 optimal weight: 0.0570 chunk 201 optimal weight: 7.9990 chunk 288 optimal weight: 0.0270 chunk 18 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 ASN D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087488 restraints weight = 55579.594| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.61 r_work: 0.2971 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33792 Z= 0.130 Angle : 0.487 9.203 46104 Z= 0.252 Chirality : 0.043 0.158 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.438 31.316 4484 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 1.32 % Allowed : 15.36 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.01 (0.13), residues: 4080 helix: 0.58 (0.24), residues: 524 sheet: 0.40 (0.14), residues: 1432 loop : -0.36 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 909 TYR 0.012 0.001 TYR A1016 PHE 0.007 0.001 PHE D 225 TRP 0.018 0.001 TRP C 90 HIS 0.003 0.001 HIS A 653 Details of bonding type rmsd covalent geometry : bond 0.00305 (33792) covalent geometry : angle 0.48664 (46104) hydrogen bonds : bond 0.02836 ( 1132) hydrogen bonds : angle 4.56634 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.331 Fit side-chains REVERT: A 40 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: A 92 MET cc_start: 0.8491 (mmm) cc_final: 0.7902 (mmp) REVERT: A 906 TYR cc_start: 0.8883 (m-80) cc_final: 0.8274 (m-80) REVERT: A 910 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 958 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7635 (p0) REVERT: B 40 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: B 92 MET cc_start: 0.8511 (mmm) cc_final: 0.7929 (mmp) REVERT: B 906 TYR cc_start: 0.8896 (m-80) cc_final: 0.8283 (m-80) REVERT: B 910 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8657 (pp) REVERT: B 958 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.7637 (p0) REVERT: C 40 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: C 92 MET cc_start: 0.8480 (mmm) cc_final: 0.7911 (mmp) REVERT: C 906 TYR cc_start: 0.8896 (m-80) cc_final: 0.8284 (m-80) REVERT: C 910 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8655 (pp) REVERT: C 958 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7642 (p0) REVERT: D 40 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 92 MET cc_start: 0.8499 (mmm) cc_final: 0.7915 (mmp) REVERT: D 906 TYR cc_start: 0.8889 (m-80) cc_final: 0.8273 (m-80) REVERT: D 910 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8640 (pp) REVERT: D 958 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.7635 (p0) outliers start: 46 outliers final: 32 residues processed: 246 average time/residue: 0.2098 time to fit residues: 84.4221 Evaluate side-chains 240 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 374 optimal weight: 8.9990 chunk 333 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 135 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 38 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN C 38 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 ASN D 38 ASN D 135 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087010 restraints weight = 55746.978| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.61 r_work: 0.2958 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33792 Z= 0.158 Angle : 0.500 9.350 46104 Z= 0.259 Chirality : 0.044 0.156 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.493 32.094 4484 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 1.63 % Allowed : 15.05 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % 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 aren not related in a simple way. whole: -0.04 (0.13), residues: 4080 helix: 0.57 (0.23), residues: 548 sheet: 0.27 (0.14), residues: 1472 loop : -0.32 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 909 TYR 0.012 0.002 TYR D1016 PHE 0.008 0.001 PHE C 143 TRP 0.017 0.001 TRP C 90 HIS 0.003 0.001 HIS A1015 Details of bonding type rmsd covalent geometry : bond 0.00373 (33792) covalent geometry : angle 0.50038 (46104) hydrogen bonds : bond 0.02941 ( 1132) hydrogen bonds : angle 4.61436 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6534.77 seconds wall clock time: 113 minutes 17.35 seconds (6797.35 seconds total)