Starting phenix.real_space_refine on Sat Jun 28 06:35:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bkg_16097/06_2025/8bkg_16097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bkg_16097/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bkg_16097/06_2025/8bkg_16097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bkg_16097/06_2025/8bkg_16097.map" model { file = "/net/cci-nas-00/data/ceres_data/8bkg_16097/06_2025/8bkg_16097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bkg_16097/06_2025/8bkg_16097.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 22.17, per 1000 atoms: 0.68 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: 8.14 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 5.03 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: 19.21 Time building geometry restraints manager: 9.56 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.330 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: 0.040 Extract box with map and model: 1.110 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 84.450 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.370 ------------------------------------------------------------------------------- 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 : 4.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.001 TRP B 90 HIS 0.009 0.001 HIS B 391 PHE 0.007 0.001 PHE A 274 TYR 0.014 0.001 TYR B1016 ARG 0.005 0.000 ARG C 894 Details of bonding type rmsd hydrogen bonds : bond 0.15241 ( 1132) hydrogen bonds : angle 6.25286 ( 3144) covalent geometry : bond 0.00281 (33792) covalent geometry : angle 0.57231 (46104) *********************** 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 : 3.854 Fit side-chains outliers start: 20 outliers final: 20 residues processed: 228 average time/residue: 0.4907 time to fit residues: 183.1305 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 : 3.639 ------------------------------------------------------------------------------- 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 344 optimal weight: 9.9990 chunk 309 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 990 HIS 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 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 990 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.089246 restraints weight = 55292.662| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.61 r_work: 0.3000 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33792 Z= 0.226 Angle : 0.570 9.329 46104 Z= 0.296 Chirality : 0.046 0.151 4820 Planarity : 0.005 0.044 6088 Dihedral : 4.848 41.219 4496 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 13.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4080 helix: -0.22 (0.22), residues: 524 sheet: 0.26 (0.14), residues: 1460 loop : -0.30 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 695 HIS 0.007 0.002 HIS D 653 PHE 0.011 0.002 PHE B 225 TYR 0.014 0.002 TYR D 123 ARG 0.006 0.001 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1132) hydrogen bonds : angle 4.81080 ( 3144) covalent geometry : bond 0.00528 (33792) covalent geometry : angle 0.57043 (46104) *********************** 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 300 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 6.571 Fit side-chains REVERT: A 92 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7815 (mmm) REVERT: A 226 HIS cc_start: 0.7382 (m170) cc_final: 0.7176 (m170) REVERT: A 671 ASP cc_start: 0.8144 (t0) cc_final: 0.7903 (t0) REVERT: A 910 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B 92 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7807 (mmm) REVERT: B 226 HIS cc_start: 0.7408 (m170) cc_final: 0.7205 (m170) REVERT: B 671 ASP cc_start: 0.8143 (t0) cc_final: 0.7904 (t0) REVERT: B 910 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8480 (pp) REVERT: C 92 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7829 (mmm) REVERT: C 226 HIS cc_start: 0.7398 (m170) cc_final: 0.7192 (m170) REVERT: C 671 ASP cc_start: 0.8143 (t0) cc_final: 0.7902 (t0) REVERT: C 910 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8483 (pp) REVERT: D 92 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7835 (mmm) REVERT: D 226 HIS cc_start: 0.7400 (m170) cc_final: 0.7195 (m170) REVERT: D 671 ASP cc_start: 0.8113 (t0) cc_final: 0.7874 (t0) REVERT: D 910 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8478 (pp) outliers start: 72 outliers final: 32 residues processed: 284 average time/residue: 0.5498 time to fit residues: 252.6222 Evaluate side-chains 244 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 3.498 ------------------------------------------------------------------------------- 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 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 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 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 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 335 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 chunk 336 optimal weight: 6.9990 chunk 383 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 263 optimal weight: 0.0270 chunk 154 optimal weight: 7.9990 chunk 397 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 overall best weight: 3.7244 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087709 restraints weight = 55683.233| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.61 r_work: 0.2975 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33792 Z= 0.190 Angle : 0.528 9.595 46104 Z= 0.274 Chirality : 0.045 0.153 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.652 36.925 4488 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.12 % Allowed : 14.36 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4080 helix: 0.06 (0.23), residues: 524 sheet: 0.29 (0.14), residues: 1472 loop : -0.25 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 90 HIS 0.005 0.001 HIS B 316 PHE 0.009 0.001 PHE B 225 TYR 0.013 0.002 TYR C 588 ARG 0.005 0.001 ARG C 909 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1132) hydrogen bonds : angle 4.72340 ( 3144) covalent geometry : bond 0.00445 (33792) covalent geometry : angle 0.52752 (46104) *********************** 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 290 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 3.997 Fit side-chains REVERT: A 438 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: A 910 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8540 (pp) REVERT: B 438 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: B 910 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8536 (pp) REVERT: C 438 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: C 910 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8544 (pp) REVERT: D 438 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: D 910 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8540 (pp) outliers start: 74 outliers final: 44 residues processed: 276 average time/residue: 0.4775 time to fit residues: 217.7712 Evaluate side-chains 252 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 200 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 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 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 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 103 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 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 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 103 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 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 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 103 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 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 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 79 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 718 GLN A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN B 135 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 GLN B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 ASN C 135 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 GLN C 739 HIS ** 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 718 GLN D 739 HIS ** D 783 GLN ** 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 = 0.3203 r_free = 0.3203 target = 0.096709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.084725 restraints weight = 56216.283| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.63 r_work: 0.2927 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 33792 Z= 0.297 Angle : 0.617 9.835 46104 Z= 0.321 Chirality : 0.048 0.166 4820 Planarity : 0.005 0.043 6088 Dihedral : 5.058 39.515 4484 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 3.15 % Allowed : 14.13 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4080 helix: -0.12 (0.23), residues: 524 sheet: 0.23 (0.13), residues: 1460 loop : -0.40 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 90 HIS 0.006 0.001 HIS C1015 PHE 0.015 0.002 PHE A 143 TYR 0.019 0.002 TYR C 588 ARG 0.006 0.001 ARG B 909 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1132) hydrogen bonds : angle 5.01497 ( 3144) covalent geometry : bond 0.00701 (33792) covalent geometry : angle 0.61714 (46104) *********************** 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 310 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 200 time to evaluate : 3.787 Fit side-chains REVERT: A 40 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: A 92 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7778 (mmp) REVERT: A 214 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 438 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 804 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8602 (t0) REVERT: A 836 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8545 (mm) REVERT: A 906 TYR cc_start: 0.8882 (m-80) cc_final: 0.8394 (m-80) REVERT: A 910 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8648 (pp) REVERT: A 958 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8065 (p0) REVERT: B 40 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 92 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8124 (mmp) REVERT: B 214 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8603 (mp) REVERT: B 438 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 804 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8598 (t0) REVERT: B 836 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8553 (mm) REVERT: B 906 TYR cc_start: 0.8885 (m-80) cc_final: 0.8398 (m-80) REVERT: B 910 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8647 (pp) REVERT: B 958 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8066 (p0) REVERT: C 40 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: C 92 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7755 (mmp) REVERT: C 214 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8602 (mp) REVERT: C 438 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: C 804 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8604 (t0) REVERT: C 836 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8557 (mm) REVERT: C 906 TYR cc_start: 0.8887 (m-80) cc_final: 0.8400 (m-80) REVERT: C 910 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8649 (pp) REVERT: C 958 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8065 (p0) REVERT: D 40 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: D 92 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7802 (mmp) REVERT: D 214 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8602 (mp) REVERT: D 438 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: D 804 ASN cc_start: 0.8968 (OUTLIER) cc_final: 0.8603 (t0) REVERT: D 836 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8556 (mm) REVERT: D 906 TYR cc_start: 0.8888 (m-80) cc_final: 0.8397 (m-80) REVERT: D 910 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8652 (pp) REVERT: D 958 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8061 (p0) outliers start: 110 outliers final: 54 residues processed: 288 average time/residue: 0.4525 time to fit residues: 216.7844 Evaluate side-chains 278 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 192 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 214 LEU 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 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU 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 103 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 214 LEU 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 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 214 LEU 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 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 214 LEU 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 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU 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 301 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 905 ASN A 958 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN 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 905 ASN 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 905 ASN D 958 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.097867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.085979 restraints weight = 55442.687| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.60 r_work: 0.2946 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33792 Z= 0.188 Angle : 0.538 9.663 46104 Z= 0.281 Chirality : 0.045 0.153 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.852 36.300 4484 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 2.37 % Allowed : 14.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4080 helix: 0.09 (0.23), residues: 524 sheet: 0.17 (0.14), residues: 1472 loop : -0.36 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 553 HIS 0.004 0.001 HIS B1015 PHE 0.009 0.001 PHE A 143 TYR 0.012 0.002 TYR C 123 ARG 0.004 0.000 ARG B 909 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 1132) hydrogen bonds : angle 4.87678 ( 3144) covalent geometry : bond 0.00442 (33792) covalent geometry : angle 0.53825 (46104) *********************** 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 287 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 204 time to evaluate : 4.125 Fit side-chains REVERT: A 92 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7757 (mmp) REVERT: A 804 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8609 (t0) REVERT: A 836 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8547 (mm) REVERT: A 906 TYR cc_start: 0.8913 (m-80) cc_final: 0.8375 (m-80) REVERT: A 910 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8646 (pp) REVERT: A 958 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8229 (p0) REVERT: A 984 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8604 (tp) REVERT: B 92 MET cc_start: 0.8466 (mmm) cc_final: 0.7796 (mmp) REVERT: B 804 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8605 (t0) REVERT: B 836 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 906 TYR cc_start: 0.8922 (m-80) cc_final: 0.8383 (m-80) REVERT: B 910 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8648 (pp) REVERT: B 958 ASN cc_start: 0.8454 (OUTLIER) cc_final: 0.8183 (p0) REVERT: B 984 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8618 (tp) REVERT: C 92 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7752 (mmp) REVERT: C 804 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8608 (t0) REVERT: C 836 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8560 (mm) REVERT: C 906 TYR cc_start: 0.8921 (m-80) cc_final: 0.8382 (m-80) REVERT: C 910 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8653 (pp) REVERT: C 958 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8189 (p0) REVERT: C 984 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8610 (tp) REVERT: D 92 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7804 (mmp) REVERT: D 804 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8615 (t0) REVERT: D 836 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8561 (mm) REVERT: D 906 TYR cc_start: 0.8918 (m-80) cc_final: 0.8377 (m-80) REVERT: D 910 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8650 (pp) REVERT: D 958 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8220 (p0) REVERT: D 984 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8605 (tp) outliers start: 83 outliers final: 36 residues processed: 272 average time/residue: 0.5322 time to fit residues: 243.4115 Evaluate side-chains 259 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 200 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 391 HIS 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 804 ASN Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 391 HIS 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 804 ASN Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 391 HIS 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 804 ASN Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 391 HIS 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 804 ASN Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 984 LEU 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 41 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 358 optimal weight: 0.0570 chunk 241 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 863 GLN A 958 ASN A1022 GLN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN B 958 ASN B1022 GLN C 135 GLN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN C 958 ASN C1022 GLN D 135 GLN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 ASN D1022 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.086595 restraints weight = 55529.335| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.61 r_work: 0.2956 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2271 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= 0.148 Angle : 0.504 9.470 46104 Z= 0.262 Chirality : 0.044 0.149 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.672 33.323 4484 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 2.86 % Allowed : 14.59 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 4080 helix: 0.27 (0.23), residues: 524 sheet: 0.23 (0.14), residues: 1464 loop : -0.35 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 553 HIS 0.003 0.001 HIS A 653 PHE 0.010 0.001 PHE C 957 TYR 0.011 0.002 TYR B 123 ARG 0.002 0.000 ARG C 909 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 1132) hydrogen bonds : angle 4.73584 ( 3144) covalent geometry : bond 0.00349 (33792) covalent geometry : angle 0.50354 (46104) *********************** 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 317 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 217 time to evaluate : 4.643 Fit side-chains REVERT: A 40 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 92 MET cc_start: 0.8520 (mmm) cc_final: 0.7926 (mmp) REVERT: A 804 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8614 (t0) REVERT: A 836 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8554 (mm) REVERT: A 910 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8636 (pp) REVERT: A 958 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7928 (p0) REVERT: B 40 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: B 92 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7886 (mmp) REVERT: B 804 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8604 (t0) REVERT: B 836 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 910 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8638 (pp) REVERT: B 958 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7923 (p0) REVERT: C 40 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: C 92 MET cc_start: 0.8486 (mmm) cc_final: 0.7853 (mmp) REVERT: C 804 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8611 (t0) REVERT: C 836 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8559 (mm) REVERT: C 910 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8641 (pp) REVERT: C 958 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7928 (p0) REVERT: D 40 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: D 92 MET cc_start: 0.8538 (mmm) cc_final: 0.7952 (mmp) REVERT: D 804 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8620 (t0) REVERT: D 836 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8556 (mm) REVERT: D 910 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8637 (pp) REVERT: D 958 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.7923 (p0) outliers start: 100 outliers final: 48 residues processed: 300 average time/residue: 0.4734 time to fit residues: 234.1080 Evaluate side-chains 276 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 103 VAL 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 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 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU 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 103 VAL 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 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 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 103 VAL 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 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 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 103 VAL 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 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 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 836 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU 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 279 optimal weight: 2.9990 chunk 339 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 chunk 265 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 400 optimal weight: 6.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 958 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086074 restraints weight = 55887.595| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.60 r_work: 0.2948 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33792 Z= 0.177 Angle : 0.521 9.553 46104 Z= 0.270 Chirality : 0.044 0.154 4820 Planarity : 0.004 0.042 6088 Dihedral : 4.683 32.768 4484 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 2.77 % Allowed : 14.73 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4080 helix: 0.26 (0.23), residues: 524 sheet: 0.18 (0.14), residues: 1472 loop : -0.37 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 553 HIS 0.004 0.001 HIS D1015 PHE 0.008 0.001 PHE D 957 TYR 0.012 0.002 TYR A 123 ARG 0.003 0.000 ARG A 909 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 1132) hydrogen bonds : angle 4.74148 ( 3144) covalent geometry : bond 0.00419 (33792) covalent geometry : angle 0.52145 (46104) *********************** 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 308 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 211 time to evaluate : 3.365 Fit side-chains REVERT: A 40 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: A 92 MET cc_start: 0.8505 (mmm) cc_final: 0.7897 (mmp) REVERT: A 804 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8634 (t0) REVERT: A 836 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (mm) REVERT: A 910 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 958 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.7869 (p0) REVERT: B 40 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 92 MET cc_start: 0.8526 (mmm) cc_final: 0.7927 (mmp) REVERT: B 804 ASN cc_start: 0.8930 (OUTLIER) cc_final: 0.8624 (t0) REVERT: B 836 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8570 (mm) REVERT: B 910 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8668 (pp) REVERT: B 958 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7866 (p0) REVERT: C 40 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 92 MET cc_start: 0.8499 (mmm) cc_final: 0.7886 (mmp) REVERT: C 804 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8640 (t0) REVERT: C 836 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8572 (mm) REVERT: C 910 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8668 (pp) REVERT: C 958 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.7865 (p0) REVERT: D 40 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: D 92 MET cc_start: 0.8522 (mmm) cc_final: 0.7923 (mmp) REVERT: D 804 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8638 (t0) REVERT: D 910 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8662 (pp) REVERT: D 958 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7861 (p0) outliers start: 97 outliers final: 53 residues processed: 299 average time/residue: 0.4569 time to fit residues: 226.0346 Evaluate side-chains 276 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 204 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 391 HIS 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 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 391 HIS 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 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS 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 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 885 ASN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS 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 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 885 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU 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 284 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 397 optimal weight: 10.0000 chunk 361 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086383 restraints weight = 55697.322| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.60 r_work: 0.2954 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2369 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= 0.159 Angle : 0.510 9.249 46104 Z= 0.265 Chirality : 0.044 0.156 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.636 32.025 4484 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 2.40 % Allowed : 15.05 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.13), residues: 4080 helix: 0.34 (0.23), residues: 548 sheet: 0.21 (0.14), residues: 1464 loop : -0.34 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 553 HIS 0.003 0.001 HIS A1015 PHE 0.007 0.001 PHE A 143 TYR 0.012 0.002 TYR D 123 ARG 0.002 0.000 ARG A 909 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 1132) hydrogen bonds : angle 4.70470 ( 3144) covalent geometry : bond 0.00375 (33792) covalent geometry : angle 0.51022 (46104) *********************** 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 284 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 200 time to evaluate : 3.577 Fit side-chains REVERT: A 40 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 92 MET cc_start: 0.8506 (mmm) cc_final: 0.7929 (mmp) REVERT: A 804 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8607 (t0) REVERT: A 836 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 910 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 958 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7815 (p0) REVERT: B 40 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 92 MET cc_start: 0.8514 (mmm) cc_final: 0.7944 (mmp) REVERT: B 804 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8595 (t0) REVERT: B 836 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8571 (mm) REVERT: B 910 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 958 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7818 (p0) REVERT: C 40 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: C 92 MET cc_start: 0.8508 (mmm) cc_final: 0.7934 (mmp) REVERT: C 804 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8615 (t0) REVERT: C 836 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8572 (mm) REVERT: C 910 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8671 (pp) REVERT: C 958 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7822 (p0) REVERT: D 40 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: D 92 MET cc_start: 0.8518 (mmm) cc_final: 0.7943 (mmp) REVERT: D 804 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8616 (t0) REVERT: D 910 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8664 (pp) REVERT: D 958 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.7814 (p0) outliers start: 84 outliers final: 52 residues processed: 276 average time/residue: 0.4594 time to fit residues: 208.2858 Evaluate side-chains 271 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 391 HIS 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 729 THR Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 391 HIS 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 729 THR Chi-restraints excluded: chain B residue 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS 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 729 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 836 ILE Chi-restraints excluded: chain C residue 885 ASN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS 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 729 THR Chi-restraints excluded: chain D residue 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 885 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU 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 104 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 105 optimal weight: 0.0030 chunk 106 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 379 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 304 optimal weight: 0.1980 overall best weight: 1.3792 ------------------------------------------------------------------------------- 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.099591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.087785 restraints weight = 55224.405| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.61 r_work: 0.2977 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33792 Z= 0.104 Angle : 0.475 9.004 46104 Z= 0.247 Chirality : 0.043 0.161 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.440 29.213 4484 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 15.33 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 4080 helix: 0.51 (0.23), residues: 548 sheet: 0.22 (0.14), residues: 1464 loop : -0.27 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 553 HIS 0.003 0.001 HIS D 391 PHE 0.007 0.001 PHE A 150 TYR 0.012 0.001 TYR B 906 ARG 0.002 0.000 ARG C 183 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 1132) hydrogen bonds : angle 4.55287 ( 3144) covalent geometry : bond 0.00245 (33792) covalent geometry : angle 0.47507 (46104) *********************** 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 286 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 206 time to evaluate : 3.604 Fit side-chains REVERT: A 40 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 92 MET cc_start: 0.8502 (mmm) cc_final: 0.7961 (mmp) REVERT: A 804 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8608 (t0) REVERT: A 910 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8634 (pp) REVERT: A 958 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7737 (p0) REVERT: B 40 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: B 92 MET cc_start: 0.8511 (mmm) cc_final: 0.7976 (mmp) REVERT: B 804 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8604 (t0) REVERT: B 910 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8641 (pp) REVERT: B 958 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7677 (p0) REVERT: C 40 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: C 92 MET cc_start: 0.8510 (mmm) cc_final: 0.7970 (mmp) REVERT: C 804 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8617 (t0) REVERT: C 910 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8642 (pp) REVERT: C 958 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7680 (p0) REVERT: D 40 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: D 92 MET cc_start: 0.8510 (mmm) cc_final: 0.7970 (mmp) REVERT: D 804 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8618 (t0) REVERT: D 910 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8632 (pp) REVERT: D 958 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7672 (p0) outliers start: 80 outliers final: 44 residues processed: 274 average time/residue: 0.4743 time to fit residues: 214.4138 Evaluate side-chains 260 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 391 HIS 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 742 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 391 HIS 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 742 THR Chi-restraints excluded: chain B residue 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 391 HIS 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 742 THR Chi-restraints excluded: chain C residue 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 885 ASN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 391 HIS 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 742 THR Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 885 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU 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 58 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 397 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 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 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.085335 restraints weight = 56119.092| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.60 r_work: 0.2937 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33792 Z= 0.233 Angle : 0.559 9.421 46104 Z= 0.290 Chirality : 0.046 0.167 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.752 33.331 4484 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.09 % Allowed : 15.62 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4080 helix: 0.28 (0.23), residues: 548 sheet: 0.16 (0.14), residues: 1472 loop : -0.37 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 90 HIS 0.005 0.001 HIS A1015 PHE 0.011 0.001 PHE A 143 TYR 0.015 0.002 TYR B 588 ARG 0.004 0.001 ARG D 909 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 1132) hydrogen bonds : angle 4.79280 ( 3144) covalent geometry : bond 0.00549 (33792) covalent geometry : angle 0.55871 (46104) ********************** 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 280 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 5.910 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 92 MET cc_start: 0.8509 (mmm) cc_final: 0.7930 (mmp) REVERT: A 804 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8620 (t0) REVERT: A 910 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 958 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.7884 (p0) REVERT: B 40 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: B 92 MET cc_start: 0.8522 (mmm) cc_final: 0.7950 (mmp) REVERT: B 804 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8608 (t0) REVERT: B 910 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8708 (pp) REVERT: B 958 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.7881 (p0) REVERT: C 40 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 92 MET cc_start: 0.8502 (mmm) cc_final: 0.7916 (mmp) REVERT: C 804 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8620 (t0) REVERT: C 910 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8710 (pp) REVERT: C 958 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.7889 (p0) REVERT: D 40 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: D 92 MET cc_start: 0.8518 (mmm) cc_final: 0.7942 (mmp) REVERT: D 804 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8632 (t0) REVERT: D 910 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8700 (pp) REVERT: D 958 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.7880 (p0) outliers start: 73 outliers final: 42 residues processed: 271 average time/residue: 0.5028 time to fit residues: 227.5635 Evaluate side-chains 257 residues out of total 3496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 202 MET 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 804 ASN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 958 ASN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 VAL 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 804 ASN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 885 ASN Chi-restraints excluded: chain B residue 910 LEU Chi-restraints excluded: chain B residue 958 ASN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 129 VAL 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 804 ASN Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 885 ASN Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 314 GLU 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 804 ASN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 885 ASN Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 958 ASN Chi-restraints excluded: chain D residue 980 GLU 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 398 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 364 optimal weight: 0.9980 chunk 302 optimal weight: 8.9990 chunk 252 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.084845 restraints weight = 56310.506| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.61 r_work: 0.2935 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33792 Z= 0.226 Angle : 0.558 9.374 46104 Z= 0.290 Chirality : 0.046 0.163 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.828 34.732 4484 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 1.95 % Allowed : 15.68 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4080 helix: 0.22 (0.23), residues: 548 sheet: 0.11 (0.14), residues: 1472 loop : -0.42 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 90 HIS 0.005 0.001 HIS B1015 PHE 0.010 0.001 PHE B 143 TYR 0.014 0.002 TYR C 123 ARG 0.004 0.001 ARG B 909 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 1132) hydrogen bonds : angle 4.85321 ( 3144) covalent geometry : bond 0.00533 (33792) covalent geometry : angle 0.55805 (46104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14320.90 seconds wall clock time: 252 minutes 56.25 seconds (15176.25 seconds total)