Starting phenix.real_space_refine on Thu Jul 31 18:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d90_30616/07_2025/7d90_30616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d90_30616/07_2025/7d90_30616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2025/7d90_30616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2025/7d90_30616.map" model { file = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2025/7d90_30616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2025/7d90_30616.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 98 5.16 5 C 8910 2.51 5 N 2266 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6815 Classifications: {'peptide': 880} Link IDs: {'PTRANS': 32, 'TRANS': 847} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B Time building chain proxies: 15.00, per 1000 atoms: 1.10 Number of scatterers: 13686 At special positions: 0 Unit cell: (108.498, 114.582, 150.072, 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 98 16.00 O 2412 8.00 N 2266 7.00 C 8910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 653 " distance=2.03 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 410 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 653 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 420 " distance=2.03 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 Links applied NAG-ASN " NAG A1201 " - " ASN A 379 " " NAG A1202 " - " ASN A 428 " " NAG B1201 " - " ASN B 379 " " NAG B1202 " - " ASN B 428 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.9 seconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 59.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.509A pdb=" N TYR A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.514A pdb=" N ASN A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.508A pdb=" N ARG A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 244 removed outlier: 3.680A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 233 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 234 " --> pdb=" O CYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.598A pdb=" N ALA A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 294 removed outlier: 3.752A pdb=" N GLY A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 335 removed outlier: 3.660A pdb=" N VAL A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.611A pdb=" N VAL A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 366 removed outlier: 3.578A pdb=" N PHE A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.531A pdb=" N GLY A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.917A pdb=" N HIS A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 removed outlier: 3.508A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 498 through 504 removed outlier: 3.859A pdb=" N SER A 503 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 504 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 540 Proline residue: A 517 - end of helix removed outlier: 3.702A pdb=" N THR A 520 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 549 through 553 removed outlier: 4.096A pdb=" N GLY A 552 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 553' Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 568 through 600 removed outlier: 3.997A pdb=" N ILE A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) Proline residue: A 592 - end of helix removed outlier: 3.733A pdb=" N GLN A 596 " --> pdb=" O PRO A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.634A pdb=" N ARG A 608 " --> pdb=" O PRO A 605 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL A 609 " --> pdb=" O PHE A 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 610 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 612 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.944A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 633 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 634 " --> pdb=" O ALA A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 667 Proline residue: A 644 - end of helix removed outlier: 3.601A pdb=" N PHE A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 699 removed outlier: 4.019A pdb=" N SER A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 697 " --> pdb=" O ALA A 693 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 726 removed outlier: 4.050A pdb=" N VAL A 705 " --> pdb=" O TYR A 701 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS A 724 " --> pdb=" O GLN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 743 removed outlier: 4.039A pdb=" N SER A 734 " --> pdb=" O ILE A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 782 removed outlier: 3.686A pdb=" N SER A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.962A pdb=" N GLN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 845 removed outlier: 3.733A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 844 " --> pdb=" O SER A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 886 removed outlier: 3.707A pdb=" N VAL A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.552A pdb=" N PHE A 899 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 932 Proline residue: A 927 - end of helix removed outlier: 3.542A pdb=" N LYS A 931 " --> pdb=" O PRO A 927 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN A 932 " --> pdb=" O PHE A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 967 Processing helix chain 'A' and resid 983 through 993 removed outlier: 4.435A pdb=" N GLU A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1099 removed outlier: 3.819A pdb=" N THR A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A1088 " --> pdb=" O MET A1084 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1129 removed outlier: 3.564A pdb=" N MET A1122 " --> pdb=" O ASP A1118 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE A1124 " --> pdb=" O ASN A1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N TYR B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 removed outlier: 3.514A pdb=" N ASN B 198 " --> pdb=" O PRO B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 removed outlier: 3.508A pdb=" N ARG B 207 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 244 removed outlier: 3.680A pdb=" N VAL B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 225 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 233 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 234 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.598A pdb=" N ALA B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 294 removed outlier: 3.752A pdb=" N GLY B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 335 removed outlier: 3.660A pdb=" N VAL B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 322 " --> pdb=" O MET B 318 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.611A pdb=" N VAL B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 366 removed outlier: 3.578A pdb=" N PHE B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 354 " --> pdb=" O CYS B 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 358 " --> pdb=" O SER B 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.531A pdb=" N GLY B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.917A pdb=" N HIS B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.508A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 498 through 504 removed outlier: 3.859A pdb=" N SER B 503 " --> pdb=" O MET B 500 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 504 " --> pdb=" O ALA B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 511 through 540 Proline residue: B 517 - end of helix removed outlier: 3.702A pdb=" N THR B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 521 " --> pdb=" O PRO B 517 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 523 " --> pdb=" O GLY B 519 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 549 through 553 removed outlier: 4.096A pdb=" N GLY B 552 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 553 " --> pdb=" O LYS B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 549 through 553' Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 568 through 600 removed outlier: 3.997A pdb=" N ILE B 572 " --> pdb=" O SER B 568 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 590 " --> pdb=" O GLN B 586 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Proline residue: B 592 - end of helix removed outlier: 3.738A pdb=" N GLN B 596 " --> pdb=" O PRO B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.634A pdb=" N ARG B 608 " --> pdb=" O PRO B 605 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL B 609 " --> pdb=" O PHE B 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 610 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS B 612 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 635 removed outlier: 3.944A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 634 " --> pdb=" O ALA B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 667 Proline residue: B 644 - end of helix removed outlier: 3.601A pdb=" N PHE B 649 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 4.019A pdb=" N SER B 684 " --> pdb=" O HIS B 680 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 699 " --> pdb=" O MET B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 726 removed outlier: 4.050A pdb=" N VAL B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 722 " --> pdb=" O GLU B 718 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 743 removed outlier: 4.039A pdb=" N SER B 734 " --> pdb=" O ILE B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 782 removed outlier: 3.686A pdb=" N SER B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 819 removed outlier: 3.962A pdb=" N GLN B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR B 813 " --> pdb=" O ALA B 809 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 845 removed outlier: 3.733A pdb=" N ILE B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN B 844 " --> pdb=" O SER B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 886 removed outlier: 3.707A pdb=" N VAL B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 882 " --> pdb=" O GLY B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 899 removed outlier: 3.552A pdb=" N PHE B 899 " --> pdb=" O ILE B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 932 Proline residue: B 927 - end of helix removed outlier: 3.542A pdb=" N LYS B 931 " --> pdb=" O PRO B 927 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN B 932 " --> pdb=" O PHE B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 967 Processing helix chain 'B' and resid 983 through 993 removed outlier: 4.435A pdb=" N GLU B 989 " --> pdb=" O ALA B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1099 removed outlier: 3.819A pdb=" N THR B1086 " --> pdb=" O ARG B1082 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B1088 " --> pdb=" O MET B1084 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B1089 " --> pdb=" O HIS B1085 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B1093 " --> pdb=" O LYS B1089 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1129 removed outlier: 3.564A pdb=" N MET B1122 " --> pdb=" O ASP B1118 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE B1124 " --> pdb=" O ASN B1120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 376 Processing sheet with id=AA2, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA3, first strand: chain 'A' and resid 826 through 832 removed outlier: 6.530A pdb=" N THR A 790 " --> pdb=" O PHE A 826 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLN A 828 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 792 " --> pdb=" O GLN A 828 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL A 830 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER A 794 " --> pdb=" O VAL A 830 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA A 832 " --> pdb=" O SER A 794 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE A 796 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 760 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 856 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA A 893 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET A 858 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A1135 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU A1136 " --> pdb=" O LYS A1102 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A1104 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A1138 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A1106 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N GLU A 908 " --> pdb=" O ALA A1101 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU A1103 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN A 910 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU A1105 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP A 912 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN A1107 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 907 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER A 940 " --> pdb=" O SER A 907 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY A 909 " --> pdb=" O SER A 940 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG A 942 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 911 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE A 944 " --> pdb=" O ILE A 911 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL A 913 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 946 " --> pdb=" O VAL A 913 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 376 Processing sheet with id=AA5, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AA6, first strand: chain 'B' and resid 826 through 832 removed outlier: 6.530A pdb=" N THR B 790 " --> pdb=" O PHE B 826 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLN B 828 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 792 " --> pdb=" O GLN B 828 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL B 830 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER B 794 " --> pdb=" O VAL B 830 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 832 " --> pdb=" O SER B 794 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE B 796 " --> pdb=" O ALA B 832 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 760 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL B 856 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA B 893 " --> pdb=" O VAL B 856 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N MET B 858 " --> pdb=" O ALA B 893 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B1135 " --> pdb=" O LYS B 894 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU B1136 " --> pdb=" O LYS B1102 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B1104 " --> pdb=" O LEU B1136 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B1138 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1106 " --> pdb=" O VAL B1138 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N GLU B 908 " --> pdb=" O ALA B1101 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU B1103 " --> pdb=" O GLU B 908 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN B 910 " --> pdb=" O LEU B1103 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU B1105 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 912 " --> pdb=" O LEU B1105 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN B1107 " --> pdb=" O ASP B 912 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER B 907 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER B 940 " --> pdb=" O SER B 907 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY B 909 " --> pdb=" O SER B 940 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG B 942 " --> pdb=" O GLY B 909 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE B 911 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE B 944 " --> pdb=" O ILE B 911 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N VAL B 913 " --> pdb=" O PHE B 944 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 946 " --> pdb=" O VAL B 913 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1764 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: 3.99 Time building geometry restraints manager: 3.69 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: 4252 1.34 - 1.46: 3400 1.46 - 1.59: 6194 1.59 - 1.71: 0 1.71 - 1.83: 158 Bond restraints: 14004 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG B1201 " pdb=" O5 NAG B1201 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA ARG A 548 " pdb=" C ARG A 548 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.64e+00 bond pdb=" CA ARG B 548 " pdb=" C ARG B 548 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.64e+00 bond pdb=" C HIS B 386 " pdb=" N ILE B 387 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.20e-02 6.94e+03 6.06e+00 ... (remaining 13999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17802 1.92 - 3.83: 1024 3.83 - 5.75: 142 5.75 - 7.67: 30 7.67 - 9.59: 16 Bond angle restraints: 19014 Sorted by residual: angle pdb=" C SER A 515 " pdb=" N ILE A 516 " pdb=" CA ILE A 516 " ideal model delta sigma weight residual 120.24 124.95 -4.71 6.30e-01 2.52e+00 5.58e+01 angle pdb=" C SER B 515 " pdb=" N ILE B 516 " pdb=" CA ILE B 516 " ideal model delta sigma weight residual 120.24 124.95 -4.71 6.30e-01 2.52e+00 5.58e+01 angle pdb=" N ARG A 593 " pdb=" CA ARG A 593 " pdb=" C ARG A 593 " ideal model delta sigma weight residual 111.36 117.64 -6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" N ARG B 593 " pdb=" CA ARG B 593 " pdb=" C ARG B 593 " ideal model delta sigma weight residual 111.36 117.58 -6.22 1.09e+00 8.42e-01 3.26e+01 angle pdb=" C ILE A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 19009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 7802 15.85 - 31.70: 402 31.70 - 47.54: 76 47.54 - 63.39: 8 63.39 - 79.24: 4 Dihedral angle restraints: 8292 sinusoidal: 3246 harmonic: 5046 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 653 " pdb=" CB CYS A 653 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 271 " pdb=" SG CYS B 271 " pdb=" SG CYS B 653 " pdb=" CB CYS B 653 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA SER A 471 " pdb=" C SER A 471 " pdb=" N LEU A 472 " pdb=" CA LEU A 472 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 8289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1596 0.054 - 0.108: 508 0.108 - 0.161: 94 0.161 - 0.215: 18 0.215 - 0.269: 4 Chirality restraints: 2220 Sorted by residual: chirality pdb=" C4 NAG B1201 " pdb=" C3 NAG B1201 " pdb=" C5 NAG B1201 " pdb=" O4 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C4 NAG A1201 " pdb=" C3 NAG A1201 " pdb=" C5 NAG A1201 " pdb=" O4 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG A 593 " pdb=" N ARG A 593 " pdb=" C ARG A 593 " pdb=" CB ARG A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2217 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 643 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 644 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 643 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 644 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 826 " 0.016 2.00e-02 2.50e+03 1.56e-02 4.23e+00 pdb=" CG PHE B 826 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 826 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 826 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 826 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 826 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 826 " 0.002 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1210 2.73 - 3.27: 13751 3.27 - 3.81: 21977 3.81 - 4.36: 26266 4.36 - 4.90: 43243 Nonbonded interactions: 106447 Sorted by model distance: nonbonded pdb=" O LEU B 588 " pdb=" CD PRO B 592 " model vdw 2.186 3.440 nonbonded pdb=" O LEU A 588 " pdb=" CD PRO A 592 " model vdw 2.189 3.440 nonbonded pdb=" OG SER A 465 " pdb=" O6 NAG A1201 " model vdw 2.234 3.040 nonbonded pdb=" OG SER B 465 " pdb=" O6 NAG B1201 " model vdw 2.234 3.040 nonbonded pdb=" O ASP A 959 " pdb=" OG1 THR A 962 " model vdw 2.253 3.040 ... (remaining 106442 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.360 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.007 0.074 14014 Z= 0.323 Angle : 1.066 9.586 19038 Z= 0.610 Chirality : 0.055 0.269 2220 Planarity : 0.007 0.054 2358 Dihedral : 10.065 79.240 5034 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.15), residues: 1752 helix: -3.77 (0.10), residues: 870 sheet: -1.42 (0.44), residues: 126 loop : -2.94 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 406 HIS 0.012 0.003 HIS B 841 PHE 0.036 0.003 PHE B 826 TYR 0.014 0.003 TYR A 701 ARG 0.015 0.001 ARG A 968 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 4) link_NAG-ASN : angle 5.00976 ( 12) hydrogen bonds : bond 0.30990 ( 612) hydrogen bonds : angle 9.80928 ( 1764) SS BOND : bond 0.00271 ( 6) SS BOND : angle 2.02762 ( 12) covalent geometry : bond 0.00684 (14004) covalent geometry : angle 1.05833 (19014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8631 (mm) cc_final: 0.8399 (tp) REVERT: A 314 MET cc_start: 0.8494 (tpt) cc_final: 0.8277 (tpt) REVERT: A 469 LEU cc_start: 0.7369 (tp) cc_final: 0.7041 (mp) REVERT: A 532 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 292 LEU cc_start: 0.8621 (mm) cc_final: 0.8387 (tp) REVERT: B 314 MET cc_start: 0.8483 (tpt) cc_final: 0.8264 (tpt) REVERT: B 469 LEU cc_start: 0.7362 (tp) cc_final: 0.7028 (mp) REVERT: B 532 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.2649 time to fit residues: 144.5500 Evaluate side-chains 215 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 513 GLN A 596 GLN A 658 ASN A 680 HIS A 751 HIS A 933 HIS A 966 HIS ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 513 GLN B 596 GLN B 658 ASN B 680 HIS B 751 HIS B 933 HIS B 966 HIS ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.099428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.086007 restraints weight = 54360.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.087871 restraints weight = 31131.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089117 restraints weight = 21089.295| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14014 Z= 0.190 Angle : 0.746 9.257 19038 Z= 0.390 Chirality : 0.045 0.200 2220 Planarity : 0.005 0.037 2358 Dihedral : 6.496 59.858 1960 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.33 % Allowed : 11.56 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.17), residues: 1752 helix: -1.54 (0.14), residues: 954 sheet: -1.14 (0.40), residues: 140 loop : -2.94 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 406 HIS 0.010 0.002 HIS A 966 PHE 0.033 0.002 PHE A 538 TYR 0.014 0.002 TYR A 273 ARG 0.005 0.001 ARG B 675 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 4) link_NAG-ASN : angle 4.29593 ( 12) hydrogen bonds : bond 0.05095 ( 612) hydrogen bonds : angle 5.25005 ( 1764) SS BOND : bond 0.00392 ( 6) SS BOND : angle 5.11007 ( 12) covalent geometry : bond 0.00417 (14004) covalent geometry : angle 0.72765 (19014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLU cc_start: 0.8440 (mp0) cc_final: 0.8207 (mp0) REVERT: A 532 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8122 (mt) REVERT: A 655 LEU cc_start: 0.9334 (tp) cc_final: 0.9119 (tp) REVERT: A 924 MET cc_start: 0.8667 (mmm) cc_final: 0.8423 (mpp) REVERT: B 456 GLU cc_start: 0.8426 (mp0) cc_final: 0.8208 (mp0) REVERT: B 532 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8115 (mt) REVERT: B 655 LEU cc_start: 0.9334 (tp) cc_final: 0.9081 (tp) REVERT: B 695 MET cc_start: 0.8330 (mtp) cc_final: 0.8043 (mtp) REVERT: B 924 MET cc_start: 0.8680 (mmm) cc_final: 0.8419 (mpp) outliers start: 49 outliers final: 13 residues processed: 274 average time/residue: 0.2039 time to fit residues: 87.0071 Evaluate side-chains 218 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 30.0000 chunk 160 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.097874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.084384 restraints weight = 56255.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086092 restraints weight = 33885.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.087298 restraints weight = 23863.749| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.184 14014 Z= 0.258 Angle : 0.819 16.731 19038 Z= 0.413 Chirality : 0.047 0.326 2220 Planarity : 0.005 0.033 2358 Dihedral : 6.356 48.705 1960 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.01 % Allowed : 12.24 % Favored : 83.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.18), residues: 1752 helix: -0.81 (0.16), residues: 952 sheet: -1.06 (0.41), residues: 140 loop : -2.81 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 914 HIS 0.007 0.002 HIS A 770 PHE 0.023 0.002 PHE A 538 TYR 0.021 0.002 TYR B 273 ARG 0.008 0.001 ARG A1139 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 4) link_NAG-ASN : angle 4.12013 ( 12) hydrogen bonds : bond 0.04794 ( 612) hydrogen bonds : angle 5.37043 ( 1764) SS BOND : bond 0.00911 ( 6) SS BOND : angle 6.82853 ( 12) covalent geometry : bond 0.00591 (14004) covalent geometry : angle 0.79442 (19014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLU cc_start: 0.8467 (mp0) cc_final: 0.8107 (mp0) REVERT: A 532 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 841 HIS cc_start: 0.7418 (t-90) cc_final: 0.6928 (t-90) REVERT: A 1084 MET cc_start: 0.5899 (mmt) cc_final: 0.5288 (tpp) REVERT: B 456 GLU cc_start: 0.8463 (mp0) cc_final: 0.8107 (mp0) REVERT: B 532 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 655 LEU cc_start: 0.9264 (tp) cc_final: 0.9013 (tp) REVERT: B 695 MET cc_start: 0.8253 (mtp) cc_final: 0.7781 (mtp) REVERT: B 1084 MET cc_start: 0.5896 (mmt) cc_final: 0.5262 (tpp) outliers start: 59 outliers final: 29 residues processed: 253 average time/residue: 0.2135 time to fit residues: 84.5675 Evaluate side-chains 216 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 1135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 155 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 918 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 918 HIS B1107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.098876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.085496 restraints weight = 55578.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.087292 restraints weight = 32635.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.088553 restraints weight = 22613.125| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 14014 Z= 0.169 Angle : 0.693 12.229 19038 Z= 0.348 Chirality : 0.044 0.293 2220 Planarity : 0.004 0.036 2358 Dihedral : 5.667 29.878 1960 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.81 % Allowed : 14.90 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 1752 helix: -0.30 (0.16), residues: 932 sheet: -1.04 (0.41), residues: 142 loop : -2.68 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 873 HIS 0.006 0.001 HIS A 841 PHE 0.021 0.002 PHE A 538 TYR 0.015 0.002 TYR B 273 ARG 0.003 0.000 ARG B 881 Details of bonding type rmsd link_NAG-ASN : bond 0.00145 ( 4) link_NAG-ASN : angle 3.75839 ( 12) hydrogen bonds : bond 0.03844 ( 612) hydrogen bonds : angle 5.03507 ( 1764) SS BOND : bond 0.00323 ( 6) SS BOND : angle 4.97105 ( 12) covalent geometry : bond 0.00391 (14004) covalent geometry : angle 0.67558 (19014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 GLU cc_start: 0.8365 (mp0) cc_final: 0.8093 (mp0) REVERT: A 532 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 1084 MET cc_start: 0.5737 (mmt) cc_final: 0.5318 (tpp) REVERT: B 456 GLU cc_start: 0.8366 (mp0) cc_final: 0.8089 (mp0) REVERT: B 532 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 655 LEU cc_start: 0.9056 (tp) cc_final: 0.8715 (tp) REVERT: B 695 MET cc_start: 0.8229 (mtp) cc_final: 0.7994 (mtp) REVERT: B 1084 MET cc_start: 0.5698 (mmt) cc_final: 0.5253 (tpp) outliers start: 56 outliers final: 33 residues processed: 265 average time/residue: 0.2007 time to fit residues: 84.3556 Evaluate side-chains 233 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.099109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.085870 restraints weight = 55226.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.087620 restraints weight = 32449.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088855 restraints weight = 22442.516| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 14014 Z= 0.171 Angle : 0.717 13.002 19038 Z= 0.357 Chirality : 0.045 0.296 2220 Planarity : 0.004 0.041 2358 Dihedral : 5.483 30.148 1960 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.63 % Allowed : 15.71 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1752 helix: -0.10 (0.17), residues: 952 sheet: -0.95 (0.43), residues: 140 loop : -2.64 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 873 HIS 0.004 0.001 HIS A 426 PHE 0.019 0.001 PHE A 538 TYR 0.016 0.001 TYR B 965 ARG 0.003 0.000 ARG A 675 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 4) link_NAG-ASN : angle 3.62852 ( 12) hydrogen bonds : bond 0.03869 ( 612) hydrogen bonds : angle 5.06112 ( 1764) SS BOND : bond 0.00362 ( 6) SS BOND : angle 5.94565 ( 12) covalent geometry : bond 0.00402 (14004) covalent geometry : angle 0.69529 (19014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 1084 MET cc_start: 0.5556 (mmt) cc_final: 0.5202 (tpp) REVERT: A 1108 MET cc_start: 0.7937 (ppp) cc_final: 0.7391 (ppp) REVERT: B 532 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8051 (mp) REVERT: B 655 LEU cc_start: 0.9112 (tp) cc_final: 0.8828 (tp) REVERT: B 1084 MET cc_start: 0.5546 (mmt) cc_final: 0.5213 (tpp) outliers start: 68 outliers final: 39 residues processed: 261 average time/residue: 0.2091 time to fit residues: 85.2089 Evaluate side-chains 240 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 28 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.099301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.086148 restraints weight = 55491.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088001 restraints weight = 32092.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.089197 restraints weight = 21922.656| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14014 Z= 0.144 Angle : 0.691 10.797 19038 Z= 0.340 Chirality : 0.044 0.307 2220 Planarity : 0.004 0.042 2358 Dihedral : 5.279 30.197 1960 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.49 % Allowed : 16.19 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1752 helix: 0.13 (0.17), residues: 960 sheet: -0.68 (0.43), residues: 138 loop : -2.65 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 873 HIS 0.007 0.001 HIS B 918 PHE 0.018 0.001 PHE B 538 TYR 0.018 0.001 TYR B 965 ARG 0.008 0.000 ARG A 990 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 3.47630 ( 12) hydrogen bonds : bond 0.03535 ( 612) hydrogen bonds : angle 4.90638 ( 1764) SS BOND : bond 0.00319 ( 6) SS BOND : angle 2.16251 ( 12) covalent geometry : bond 0.00328 (14004) covalent geometry : angle 0.68341 (19014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 924 MET cc_start: 0.8513 (mmm) cc_final: 0.8186 (mpp) REVERT: A 1084 MET cc_start: 0.5428 (mmt) cc_final: 0.5071 (tpp) REVERT: A 1108 MET cc_start: 0.7845 (ppp) cc_final: 0.7543 (ppp) REVERT: B 532 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8021 (mp) REVERT: B 695 MET cc_start: 0.8402 (mtp) cc_final: 0.8079 (mtp) REVERT: B 924 MET cc_start: 0.8522 (mmm) cc_final: 0.8199 (mpp) REVERT: B 1084 MET cc_start: 0.5437 (mmt) cc_final: 0.5203 (tpp) outliers start: 66 outliers final: 43 residues processed: 250 average time/residue: 0.2047 time to fit residues: 80.2738 Evaluate side-chains 240 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.097855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084829 restraints weight = 56436.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.086538 restraints weight = 33600.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.087753 restraints weight = 23488.989| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 14014 Z= 0.204 Angle : 0.746 13.300 19038 Z= 0.372 Chirality : 0.046 0.308 2220 Planarity : 0.004 0.044 2358 Dihedral : 5.434 30.060 1960 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.49 % Allowed : 16.87 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 1752 helix: 0.08 (0.16), residues: 950 sheet: -0.70 (0.43), residues: 138 loop : -2.65 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 570 HIS 0.006 0.001 HIS A 841 PHE 0.015 0.002 PHE A 538 TYR 0.013 0.002 TYR B 273 ARG 0.005 0.000 ARG A 990 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 3.66596 ( 12) hydrogen bonds : bond 0.03898 ( 612) hydrogen bonds : angle 5.09491 ( 1764) SS BOND : bond 0.00656 ( 6) SS BOND : angle 6.72130 ( 12) covalent geometry : bond 0.00479 (14004) covalent geometry : angle 0.72143 (19014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 195 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8099 (mp) REVERT: A 1084 MET cc_start: 0.5426 (mmt) cc_final: 0.5047 (tpp) REVERT: B 532 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 1084 MET cc_start: 0.5436 (mmt) cc_final: 0.5141 (tpp) outliers start: 66 outliers final: 50 residues processed: 240 average time/residue: 0.2033 time to fit residues: 77.3126 Evaluate side-chains 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 169 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 135 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.100066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.086955 restraints weight = 55432.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.088761 restraints weight = 32480.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.089982 restraints weight = 22385.156| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 14014 Z= 0.138 Angle : 0.714 14.645 19038 Z= 0.348 Chirality : 0.045 0.311 2220 Planarity : 0.004 0.046 2358 Dihedral : 5.267 30.111 1960 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.61 % Allowed : 19.12 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1752 helix: 0.29 (0.16), residues: 952 sheet: -0.51 (0.45), residues: 136 loop : -2.54 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 873 HIS 0.005 0.001 HIS B 918 PHE 0.018 0.001 PHE A 538 TYR 0.009 0.001 TYR A 253 ARG 0.005 0.000 ARG A 990 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 4) link_NAG-ASN : angle 3.27026 ( 12) hydrogen bonds : bond 0.03498 ( 612) hydrogen bonds : angle 4.86160 ( 1764) SS BOND : bond 0.00328 ( 6) SS BOND : angle 5.25305 ( 12) covalent geometry : bond 0.00330 (14004) covalent geometry : angle 0.69711 (19014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 532 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8000 (mp) outliers start: 53 outliers final: 35 residues processed: 241 average time/residue: 0.2090 time to fit residues: 79.0517 Evaluate side-chains 231 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 111 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 49 optimal weight: 0.0980 chunk 18 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084400 restraints weight = 56619.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086129 restraints weight = 33580.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.087387 restraints weight = 23469.583| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14014 Z= 0.212 Angle : 0.780 12.456 19038 Z= 0.382 Chirality : 0.047 0.307 2220 Planarity : 0.004 0.046 2358 Dihedral : 5.454 30.284 1960 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.01 % Allowed : 18.98 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1752 helix: 0.17 (0.16), residues: 960 sheet: -0.67 (0.45), residues: 136 loop : -2.56 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 873 HIS 0.007 0.002 HIS B 841 PHE 0.020 0.002 PHE A 685 TYR 0.012 0.002 TYR B 273 ARG 0.004 0.001 ARG A 990 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 4) link_NAG-ASN : angle 3.66458 ( 12) hydrogen bonds : bond 0.03782 ( 612) hydrogen bonds : angle 5.05429 ( 1764) SS BOND : bond 0.00481 ( 6) SS BOND : angle 2.28231 ( 12) covalent geometry : bond 0.00475 (14004) covalent geometry : angle 0.77247 (19014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 707 MET cc_start: 0.7213 (mmm) cc_final: 0.6689 (mtm) REVERT: A 1108 MET cc_start: 0.7570 (ppp) cc_final: 0.6622 (ppp) REVERT: B 532 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8086 (mp) outliers start: 59 outliers final: 47 residues processed: 228 average time/residue: 0.2195 time to fit residues: 77.7021 Evaluate side-chains 237 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 127 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 156 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 166 optimal weight: 0.0070 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.100547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087589 restraints weight = 54346.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089427 restraints weight = 31754.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090701 restraints weight = 21726.852| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 14014 Z= 0.136 Angle : 0.737 12.081 19038 Z= 0.356 Chirality : 0.046 0.325 2220 Planarity : 0.004 0.046 2358 Dihedral : 5.233 29.901 1960 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.45 % Allowed : 20.27 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1752 helix: 0.34 (0.16), residues: 950 sheet: -0.42 (0.46), residues: 136 loop : -2.49 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 873 HIS 0.005 0.001 HIS A 816 PHE 0.023 0.001 PHE B 685 TYR 0.009 0.001 TYR A 253 ARG 0.004 0.000 ARG A 990 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 4) link_NAG-ASN : angle 3.16147 ( 12) hydrogen bonds : bond 0.03646 ( 612) hydrogen bonds : angle 4.85308 ( 1764) SS BOND : bond 0.00663 ( 6) SS BOND : angle 5.01862 ( 12) covalent geometry : bond 0.00329 (14004) covalent geometry : angle 0.72232 (19014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7091 (m-80) cc_final: 0.6734 (m-10) REVERT: A 532 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 695 MET cc_start: 0.8305 (ptp) cc_final: 0.8085 (ptp) REVERT: A 1108 MET cc_start: 0.7500 (ppp) cc_final: 0.6454 (ppp) REVERT: B 451 TYR cc_start: 0.7097 (m-80) cc_final: 0.6719 (m-10) REVERT: B 532 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7996 (mp) outliers start: 36 outliers final: 32 residues processed: 234 average time/residue: 0.2031 time to fit residues: 75.0630 Evaluate side-chains 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 63 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.100025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.087008 restraints weight = 55388.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.088808 restraints weight = 32561.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.089974 restraints weight = 22462.846| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14014 Z= 0.143 Angle : 0.748 12.789 19038 Z= 0.356 Chirality : 0.046 0.318 2220 Planarity : 0.004 0.050 2358 Dihedral : 5.137 31.257 1960 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.06 % Allowed : 20.75 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1752 helix: 0.41 (0.16), residues: 950 sheet: -0.38 (0.46), residues: 136 loop : -2.44 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 873 HIS 0.005 0.001 HIS A 816 PHE 0.031 0.001 PHE B 963 TYR 0.013 0.001 TYR B 283 ARG 0.004 0.000 ARG A 990 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 4) link_NAG-ASN : angle 3.09255 ( 12) hydrogen bonds : bond 0.03524 ( 612) hydrogen bonds : angle 4.88258 ( 1764) SS BOND : bond 0.00386 ( 6) SS BOND : angle 3.57434 ( 12) covalent geometry : bond 0.00337 (14004) covalent geometry : angle 0.73905 (19014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4155.58 seconds wall clock time: 72 minutes 53.33 seconds (4373.33 seconds total)