Starting phenix.real_space_refine on Fri Jul 3 10:38:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_30616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_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_2026/7d90_30616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_30616.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_30616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_30616.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_30616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d90_30616/07_2026/7d90_30616.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 chiralities: 2 Restraints were copied for chains: B Time building chain proxies: 5.87, per 1000 atoms: 0.43 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: 0.98 Conformation dependent library (CDL) restraints added in 484.3 milliseconds 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: 0.41 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: 2.18 Time building geometry restraints manager: 1.34 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: 7730 15.85 - 31.70: 398 31.70 - 47.54: 72 47.54 - 63.39: 4 63.39 - 79.24: 4 Dihedral angle restraints: 8208 sinusoidal: 3162 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 8205 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: 0.02 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: 1.130 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: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 9.930 79.240 4950 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.00 (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 ARG 0.015 0.001 ARG A 968 TYR 0.014 0.003 TYR A 701 PHE 0.036 0.003 PHE B 826 TRP 0.026 0.003 TRP B 406 HIS 0.012 0.003 HIS B 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.32 (14004) covalent geometry : angle 1.05833 / 0.61 (19014) SS BOND : bond 0.00271 / 0.16 ( 6) SS BOND : angle 2.02762 / 1.11 ( 12) hydrogen bonds : bond 0.30990 / 20.35 ( 612) hydrogen bonds : angle 9.80928 / 6.85 ( 1764) link_NAG-ASN : bond 0.00530 / 0.32 ( 4) link_NAG-ASN : angle 5.00976 / 3.20 ( 12) *********************** 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 : 0.509 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: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8631 (mm) cc_final: 0.8400 (tp) REVERT: A 314 MET cc_start: 0.8494 (tpt) cc_final: 0.8279 (tpt) REVERT: A 469 LEU cc_start: 0.7369 (tp) cc_final: 0.7044 (mp) REVERT: A 532 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (mt) REVERT: B 292 LEU cc_start: 0.8621 (mm) cc_final: 0.8388 (tp) REVERT: B 314 MET cc_start: 0.8483 (tpt) cc_final: 0.8267 (tpt) REVERT: B 469 LEU cc_start: 0.7362 (tp) cc_final: 0.7032 (mp) REVERT: B 532 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8027 (mt) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.1118 time to fit residues: 62.0282 Evaluate side-chains 220 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3921 r_free = 0.3921 target = 0.099527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085934 restraints weight = 55432.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.087780 restraints weight = 32297.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.089024 restraints weight = 22211.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089799 restraints weight = 17081.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090304 restraints weight = 14385.927| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14014 Z= 0.189 Angle : 0.745 9.297 19038 Z= 0.388 Chirality : 0.045 0.188 2220 Planarity : 0.005 0.036 2358 Dihedral : 6.025 31.022 1876 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.93 % Allowed : 11.63 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.17), residues: 1752 helix: -1.54 (0.14), residues: 954 sheet: -1.11 (0.41), residues: 140 loop : -2.95 (0.20), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 937 TYR 0.015 0.002 TYR B 273 PHE 0.031 0.002 PHE A 538 TRP 0.019 0.002 TRP B 406 HIS 0.011 0.002 HIS A 966 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (14004) covalent geometry : angle 0.72683 / 0.38 (19014) SS BOND : bond 0.00390 / 0.24 ( 6) SS BOND : angle 5.13271 / 2.70 ( 12) hydrogen bonds : bond 0.05189 / 3.41 ( 612) hydrogen bonds : angle 5.24885 / 3.70 ( 1764) link_NAG-ASN : bond 0.00219 / 0.13 ( 4) link_NAG-ASN : angle 4.22999 / 2.65 ( 12) *********************** 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 289 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.506 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: 0.8378 (OUTLIER) cc_final: 0.8106 (mt) REVERT: A 655 LEU cc_start: 0.9266 (tp) cc_final: 0.9019 (tp) REVERT: A 695 MET cc_start: 0.8286 (mtp) cc_final: 0.8045 (mtp) REVERT: A 712 MET cc_start: 0.7246 (ppp) cc_final: 0.7029 (ttt) REVERT: B 532 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 655 LEU cc_start: 0.9270 (tp) cc_final: 0.9022 (tp) REVERT: B 695 MET cc_start: 0.8281 (mtp) cc_final: 0.8050 (mtp) REVERT: B 712 MET cc_start: 0.7248 (ppp) cc_final: 0.7031 (ttt) outliers start: 43 outliers final: 12 residues processed: 275 average time/residue: 0.0928 time to fit residues: 40.1460 Evaluate side-chains 207 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 66 optimal weight: 0.0670 chunk 162 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 156 optimal weight: 0.0070 overall best weight: 3.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.099130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085603 restraints weight = 56250.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.087419 restraints weight = 33080.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088659 restraints weight = 22952.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.089528 restraints weight = 17723.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.090040 restraints weight = 14698.174| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 14014 Z= 0.192 Angle : 0.752 12.184 19038 Z= 0.376 Chirality : 0.045 0.255 2220 Planarity : 0.004 0.031 2358 Dihedral : 5.808 30.012 1876 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.40 % Allowed : 12.99 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.19), residues: 1752 helix: -0.70 (0.16), residues: 950 sheet: -0.90 (0.42), residues: 140 loop : -2.73 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 968 TYR 0.020 0.002 TYR B 273 PHE 0.024 0.002 PHE A 538 TRP 0.020 0.002 TRP B 915 HIS 0.006 0.002 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (14004) covalent geometry : angle 0.72726 / 0.37 (19014) SS BOND : bond 0.00452 / 0.29 ( 6) SS BOND : angle 6.66354 / 3.38 ( 12) hydrogen bonds : bond 0.04347 / 2.87 ( 612) hydrogen bonds : angle 5.08065 / 3.52 ( 1764) link_NAG-ASN : bond 0.00189 / 0.11 ( 4) link_NAG-ASN : angle 3.78209 / 2.43 ( 12) *********************** 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 265 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8180 (mt) REVERT: A 655 LEU cc_start: 0.9172 (tp) cc_final: 0.8917 (tp) REVERT: A 712 MET cc_start: 0.7453 (ppp) cc_final: 0.6968 (tmm) REVERT: A 1084 MET cc_start: 0.5693 (mmt) cc_final: 0.5219 (tpp) REVERT: B 532 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8176 (mt) REVERT: B 655 LEU cc_start: 0.9159 (tp) cc_final: 0.8905 (tp) REVERT: B 712 MET cc_start: 0.7456 (ppp) cc_final: 0.6962 (tmm) REVERT: B 1084 MET cc_start: 0.5716 (mmt) cc_final: 0.5199 (tpp) outliers start: 50 outliers final: 24 residues processed: 250 average time/residue: 0.0945 time to fit residues: 37.3603 Evaluate side-chains 215 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 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 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 326 LEU Chi-restraints excluded: chain B residue 327 VAL 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 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 71 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN A 534 ASN A 918 HIS ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN B 534 ASN B 918 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.101170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.087902 restraints weight = 55028.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.089690 restraints weight = 31884.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.090985 restraints weight = 21948.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.091834 restraints weight = 16729.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.092324 restraints weight = 13860.207| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14014 Z= 0.125 Angle : 0.660 11.098 19038 Z= 0.324 Chirality : 0.043 0.294 2220 Planarity : 0.004 0.035 2358 Dihedral : 5.358 29.949 1876 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.13 % Allowed : 13.81 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1752 helix: -0.16 (0.16), residues: 958 sheet: -0.50 (0.43), residues: 138 loop : -2.61 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 968 TYR 0.014 0.001 TYR B 965 PHE 0.020 0.001 PHE A 538 TRP 0.013 0.001 TRP A 915 HIS 0.004 0.001 HIS B 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14004) covalent geometry : angle 0.64765 / 0.32 (19014) SS BOND : bond 0.00214 / 0.12 ( 6) SS BOND : angle 4.00926 / 2.11 ( 12) hydrogen bonds : bond 0.03566 / 2.34 ( 612) hydrogen bonds : angle 4.73018 / 3.31 ( 1764) link_NAG-ASN : bond 0.00143 / 0.09 ( 4) link_NAG-ASN : angle 3.27976 / 2.06 ( 12) *********************** 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 272 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 695 MET cc_start: 0.8175 (mtp) cc_final: 0.7803 (mtp) REVERT: A 712 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6883 (tmm) REVERT: A 1084 MET cc_start: 0.5593 (mmt) cc_final: 0.5282 (tpp) REVERT: B 532 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 695 MET cc_start: 0.8160 (mtp) cc_final: 0.7744 (mtp) REVERT: B 712 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6891 (tmm) REVERT: B 1084 MET cc_start: 0.5585 (mmt) cc_final: 0.5253 (tpp) outliers start: 46 outliers final: 24 residues processed: 257 average time/residue: 0.0833 time to fit residues: 34.5693 Evaluate side-chains 229 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 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 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 271 CYS 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 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 712 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 152 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 GLN A 534 ASN A1107 ASN B 513 GLN B 534 ASN B1107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.101299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087851 restraints weight = 55128.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.089714 restraints weight = 31650.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.090922 restraints weight = 21607.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.091848 restraints weight = 16658.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.092278 restraints weight = 13678.840| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.003 0.116 14014 Z= 0.131 Angle : 0.671 11.175 19038 Z= 0.326 Chirality : 0.043 0.253 2220 Planarity : 0.004 0.040 2358 Dihedral : 5.190 29.686 1876 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.54 % Allowed : 14.90 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1752 helix: 0.08 (0.16), residues: 952 sheet: -0.51 (0.43), residues: 138 loop : -2.56 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 968 TYR 0.017 0.001 TYR A 965 PHE 0.017 0.001 PHE A 538 TRP 0.018 0.001 TRP B 570 HIS 0.003 0.001 HIS B 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14004) covalent geometry : angle 0.65360 / 0.32 (19014) SS BOND : bond 0.00468 / 0.29 ( 6) SS BOND : angle 5.37792 / 2.69 ( 12) hydrogen bonds : bond 0.03628 / 2.38 ( 612) hydrogen bonds : angle 4.67796 / 3.24 ( 1764) link_NAG-ASN : bond 0.00158 / 0.10 ( 4) link_NAG-ASN : angle 2.99615 / 1.90 ( 12) *********************** 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 271 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 695 MET cc_start: 0.8218 (mtp) cc_final: 0.7948 (mpp) REVERT: A 712 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6783 (tmm) REVERT: B 532 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8213 (mt) REVERT: B 695 MET cc_start: 0.8220 (mtp) cc_final: 0.8005 (mpp) REVERT: B 712 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6841 (tmm) outliers start: 52 outliers final: 31 residues processed: 249 average time/residue: 0.0936 time to fit residues: 36.7119 Evaluate side-chains 231 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 295 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 LEU 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 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 328 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 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 66 optimal weight: 0.0980 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 GLN A 534 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 534 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.100801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.087495 restraints weight = 54771.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.089313 restraints weight = 32221.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090571 restraints weight = 22287.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.091382 restraints weight = 17129.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.092019 restraints weight = 14239.319| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14014 Z= 0.128 Angle : 0.669 8.808 19038 Z= 0.324 Chirality : 0.043 0.271 2220 Planarity : 0.004 0.042 2358 Dihedral : 5.005 28.858 1876 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.29 % Allowed : 14.90 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1752 helix: 0.32 (0.16), residues: 946 sheet: -0.41 (0.43), residues: 138 loop : -2.50 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 968 TYR 0.011 0.001 TYR B 253 PHE 0.020 0.001 PHE B 538 TRP 0.012 0.001 TRP B 873 HIS 0.007 0.001 HIS A 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (14004) covalent geometry : angle 0.66424 / 0.32 (19014) SS BOND : bond 0.00403 / 0.25 ( 6) SS BOND : angle 1.83171 / 1.01 ( 12) hydrogen bonds : bond 0.03418 / 2.21 ( 612) hydrogen bonds : angle 4.56926 / 3.19 ( 1764) link_NAG-ASN : bond 0.00153 / 0.09 ( 4) link_NAG-ASN : angle 2.88245 / 1.85 ( 12) *********************** 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 264 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 201 time to evaluate : 0.614 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: 0.8440 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 712 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6755 (tmm) REVERT: B 532 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 695 MET cc_start: 0.8274 (mtp) cc_final: 0.7971 (mtt) REVERT: B 712 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6813 (tmm) outliers start: 63 outliers final: 37 residues processed: 241 average time/residue: 0.0895 time to fit residues: 34.4690 Evaluate side-chains 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 513 GLN 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 712 MET 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 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 348 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 513 GLN Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 27 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** 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 = 0.3985 r_free = 0.3985 target = 0.102682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089316 restraints weight = 54885.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091140 restraints weight = 31965.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.092418 restraints weight = 21974.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093120 restraints weight = 16883.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.093825 restraints weight = 14234.774| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4953 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= 0.121 Angle : 0.684 10.110 19038 Z= 0.328 Chirality : 0.043 0.289 2220 Planarity : 0.004 0.041 2358 Dihedral : 4.949 29.012 1876 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.93 % Allowed : 17.55 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1752 helix: 0.42 (0.17), residues: 956 sheet: -0.34 (0.44), residues: 138 loop : -2.51 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.012 0.001 TYR A 253 PHE 0.019 0.001 PHE B 538 TRP 0.014 0.001 TRP B 873 HIS 0.005 0.001 HIS A 918 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14004) covalent geometry : angle 0.66932 / 0.32 (19014) SS BOND : bond 0.00988 / 0.58 ( 6) SS BOND : angle 5.04651 / 2.66 ( 12) hydrogen bonds : bond 0.03494 / 2.33 ( 612) hydrogen bonds : angle 4.52137 / 3.14 ( 1764) link_NAG-ASN : bond 0.00169 / 0.10 ( 4) link_NAG-ASN : angle 2.59069 / 1.61 ( 12) *********************** 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 240 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.310 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: 0.8412 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 712 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6835 (tmm) REVERT: B 532 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8175 (mt) REVERT: B 712 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6831 (tmm) outliers start: 43 outliers final: 28 residues processed: 227 average time/residue: 0.0764 time to fit residues: 27.8890 Evaluate side-chains 225 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 326 LEU 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 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 712 MET 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 B residue 208 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 348 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 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 712 MET 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 1128 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 25 optimal weight: 0.0470 chunk 8 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 GLN A 534 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 534 ASN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.101545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.088216 restraints weight = 55495.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.089974 restraints weight = 33126.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.091227 restraints weight = 23230.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091951 restraints weight = 18019.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.092576 restraints weight = 15180.931| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14014 Z= 0.145 Angle : 0.700 12.012 19038 Z= 0.338 Chirality : 0.044 0.300 2220 Planarity : 0.004 0.043 2358 Dihedral : 4.982 31.438 1876 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.54 % Allowed : 18.16 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1752 helix: 0.44 (0.17), residues: 948 sheet: -0.47 (0.43), residues: 138 loop : -2.35 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.011 0.001 TYR B 253 PHE 0.017 0.001 PHE B 347 TRP 0.012 0.001 TRP B 873 HIS 0.007 0.001 HIS B 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (14004) covalent geometry : angle 0.68564 / 0.33 (19014) SS BOND : bond 0.00469 / 0.27 ( 6) SS BOND : angle 5.02117 / 2.59 ( 12) hydrogen bonds : bond 0.03535 / 2.33 ( 612) hydrogen bonds : angle 4.64447 / 3.24 ( 1764) link_NAG-ASN : bond 0.00147 / 0.09 ( 4) link_NAG-ASN : angle 2.74126 / 1.77 ( 12) *********************** 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 246 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7204 (m-80) cc_final: 0.6751 (m-10) REVERT: A 532 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 712 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6763 (tmm) REVERT: B 451 TYR cc_start: 0.7202 (m-80) cc_final: 0.6739 (m-10) REVERT: B 532 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8023 (mp) REVERT: B 712 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6908 (tmm) outliers start: 52 outliers final: 38 residues processed: 227 average time/residue: 0.0803 time to fit residues: 29.4825 Evaluate side-chains 229 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 513 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 712 MET 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 945 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE 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 513 GLN Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 712 MET 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 945 THR Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 111 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 63 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 172 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 147 optimal weight: 0.4980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 918 HIS ** 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 = 0.3949 r_free = 0.3949 target = 0.100491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.087316 restraints weight = 55515.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.089086 restraints weight = 32840.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090306 restraints weight = 22843.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.091148 restraints weight = 17677.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.091617 restraints weight = 14675.962| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 14014 Z= 0.166 Angle : 0.744 10.939 19038 Z= 0.360 Chirality : 0.045 0.307 2220 Planarity : 0.004 0.049 2358 Dihedral : 5.035 29.622 1876 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.27 % Allowed : 18.84 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1752 helix: 0.38 (0.17), residues: 940 sheet: -0.62 (0.43), residues: 138 loop : -2.44 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1113 TYR 0.013 0.001 TYR B1121 PHE 0.018 0.001 PHE A 347 TRP 0.011 0.001 TRP A 873 HIS 0.008 0.001 HIS B 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (14004) covalent geometry : angle 0.72959 / 0.35 (19014) SS BOND : bond 0.00513 / 0.32 ( 6) SS BOND : angle 5.20389 / 2.66 ( 12) hydrogen bonds : bond 0.03692 / 2.43 ( 612) hydrogen bonds : angle 4.75637 / 3.31 ( 1764) link_NAG-ASN : bond 0.00163 / 0.09 ( 4) link_NAG-ASN : angle 2.89967 / 1.89 ( 12) *********************** 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 233 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7267 (m-80) cc_final: 0.6786 (m-10) REVERT: A 532 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 712 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6848 (tmm) REVERT: B 451 TYR cc_start: 0.7258 (m-80) cc_final: 0.6788 (m-10) REVERT: B 532 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 704 ILE cc_start: 0.8157 (mm) cc_final: 0.7933 (mm) REVERT: B 712 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6885 (tmm) outliers start: 48 outliers final: 38 residues processed: 216 average time/residue: 0.0845 time to fit residues: 29.6537 Evaluate side-chains 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 532 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 712 MET 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 945 THR 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 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 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 712 MET 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 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 11 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 119 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 169 optimal weight: 0.0870 chunk 105 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 513 GLN ** A 918 HIS ** 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 = 0.3986 r_free = 0.3986 target = 0.102568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.089403 restraints weight = 54830.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091241 restraints weight = 32626.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.092491 restraints weight = 22699.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093352 restraints weight = 17541.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.093920 restraints weight = 14529.441| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14014 Z= 0.112 Angle : 0.700 10.998 19038 Z= 0.331 Chirality : 0.045 0.325 2220 Planarity : 0.004 0.047 2358 Dihedral : 4.767 29.936 1876 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.52 % Allowed : 19.46 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1752 helix: 0.61 (0.17), residues: 938 sheet: -0.52 (0.45), residues: 138 loop : -2.40 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 881 TYR 0.014 0.001 TYR B 283 PHE 0.012 0.001 PHE B 538 TRP 0.014 0.001 TRP B 873 HIS 0.008 0.001 HIS B 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14004) covalent geometry : angle 0.69632 / 0.33 (19014) SS BOND : bond 0.00487 / 0.28 ( 6) SS BOND : angle 1.68875 / 0.98 ( 12) hydrogen bonds : bond 0.03303 / 2.15 ( 612) hydrogen bonds : angle 4.52931 / 3.16 ( 1764) link_NAG-ASN : bond 0.00141 / 0.09 ( 4) link_NAG-ASN : angle 2.53155 / 1.56 ( 12) ********************** 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 236 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7031 (m-80) cc_final: 0.6723 (m-10) REVERT: A 532 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7995 (mp) REVERT: A 712 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6839 (tmm) REVERT: B 451 TYR cc_start: 0.7017 (m-80) cc_final: 0.6724 (m-10) REVERT: B 532 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8001 (mp) REVERT: B 712 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6933 (tmm) outliers start: 37 outliers final: 30 residues processed: 228 average time/residue: 0.0908 time to fit residues: 32.7079 Evaluate side-chains 224 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 326 LEU 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 513 GLN Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 712 MET 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 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 157 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 918 HIS ** 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 = 0.3981 r_free = 0.3981 target = 0.102359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.089277 restraints weight = 54920.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.091107 restraints weight = 32392.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.092359 restraints weight = 22405.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093181 restraints weight = 17276.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.093685 restraints weight = 14346.498| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 14014 Z= 0.125 Angle : 0.732 10.917 19038 Z= 0.345 Chirality : 0.045 0.311 2220 Planarity : 0.004 0.048 2358 Dihedral : 4.767 29.995 1876 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.38 % Allowed : 19.93 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1752 helix: 0.63 (0.17), residues: 932 sheet: -0.52 (0.45), residues: 138 loop : -2.36 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.013 0.001 TYR B1121 PHE 0.031 0.001 PHE A 963 TRP 0.013 0.001 TRP B 873 HIS 0.006 0.001 HIS B 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14004) covalent geometry : angle 0.72311 / 0.34 (19014) SS BOND : bond 0.00553 / 0.34 ( 6) SS BOND : angle 3.87467 / 2.38 ( 12) hydrogen bonds : bond 0.03421 / 2.24 ( 612) hydrogen bonds : angle 4.62888 / 3.23 ( 1764) link_NAG-ASN : bond 0.00132 / 0.08 ( 4) link_NAG-ASN : angle 2.54072 / 1.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2127.13 seconds wall clock time: 37 minutes 40.35 seconds (2260.35 seconds total)