Starting phenix.real_space_refine on Wed Mar 4 12:43:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d90_30616/03_2026/7d90_30616.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d90_30616/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7d90_30616/03_2026/7d90_30616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d90_30616/03_2026/7d90_30616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d90_30616/03_2026/7d90_30616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d90_30616/03_2026/7d90_30616.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B Time building chain proxies: 6.15, per 1000 atoms: 0.45 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: 1.23 Conformation dependent library (CDL) restraints added in 568.5 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: 0.49 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: 2.33 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4252 1.34 - 1.46: 3400 1.46 - 1.59: 6194 1.59 - 1.71: 0 1.71 - 1.83: 158 Bond restraints: 14004 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG B1201 " pdb=" O5 NAG B1201 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" CA ARG A 548 " pdb=" C ARG A 548 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.64e+00 bond pdb=" CA ARG B 548 " pdb=" C ARG B 548 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.64e+00 bond pdb=" C HIS B 386 " pdb=" N ILE B 387 " ideal model delta sigma weight residual 1.333 1.303 0.030 1.20e-02 6.94e+03 6.06e+00 ... (remaining 13999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 17802 1.92 - 3.83: 1024 3.83 - 5.75: 142 5.75 - 7.67: 30 7.67 - 9.59: 16 Bond angle restraints: 19014 Sorted by residual: angle pdb=" C SER A 515 " pdb=" N ILE A 516 " pdb=" CA ILE A 516 " ideal model delta sigma weight residual 120.24 124.95 -4.71 6.30e-01 2.52e+00 5.58e+01 angle pdb=" C SER B 515 " pdb=" N ILE B 516 " pdb=" CA ILE B 516 " ideal model delta sigma weight residual 120.24 124.95 -4.71 6.30e-01 2.52e+00 5.58e+01 angle pdb=" N ARG A 593 " pdb=" CA ARG A 593 " pdb=" C ARG A 593 " ideal model delta sigma weight residual 111.36 117.64 -6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" N ARG B 593 " pdb=" CA ARG B 593 " pdb=" C ARG B 593 " ideal model delta sigma weight residual 111.36 117.58 -6.22 1.09e+00 8.42e-01 3.26e+01 angle pdb=" C ILE A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 19009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 7802 15.85 - 31.70: 402 31.70 - 47.54: 76 47.54 - 63.39: 8 63.39 - 79.24: 4 Dihedral angle restraints: 8292 sinusoidal: 3246 harmonic: 5046 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 653 " pdb=" CB CYS A 653 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CB CYS B 271 " pdb=" SG CYS B 271 " pdb=" SG CYS B 653 " pdb=" CB CYS B 653 " ideal model delta sinusoidal sigma weight residual 93.00 152.90 -59.90 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA SER A 471 " pdb=" C SER A 471 " pdb=" N LEU A 472 " pdb=" CA LEU A 472 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 8289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1596 0.054 - 0.108: 508 0.108 - 0.161: 94 0.161 - 0.215: 18 0.215 - 0.269: 4 Chirality restraints: 2220 Sorted by residual: chirality pdb=" C4 NAG B1201 " pdb=" C3 NAG B1201 " pdb=" C5 NAG B1201 " pdb=" O4 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C4 NAG A1201 " pdb=" C3 NAG A1201 " pdb=" C5 NAG A1201 " pdb=" O4 NAG A1201 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG A 593 " pdb=" N ARG A 593 " pdb=" C ARG A 593 " pdb=" CB ARG A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2217 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 643 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 644 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 643 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 644 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 826 " 0.016 2.00e-02 2.50e+03 1.56e-02 4.23e+00 pdb=" CG PHE B 826 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 826 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 826 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 826 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 826 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 826 " 0.002 2.00e-02 2.50e+03 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1210 2.73 - 3.27: 13751 3.27 - 3.81: 21977 3.81 - 4.36: 26266 4.36 - 4.90: 43243 Nonbonded interactions: 106447 Sorted by model distance: nonbonded pdb=" O LEU B 588 " pdb=" CD PRO B 592 " model vdw 2.186 3.440 nonbonded pdb=" O LEU A 588 " pdb=" CD PRO A 592 " model vdw 2.189 3.440 nonbonded pdb=" OG SER A 465 " pdb=" O6 NAG A1201 " model vdw 2.234 3.040 nonbonded pdb=" OG SER B 465 " pdb=" O6 NAG B1201 " model vdw 2.234 3.040 nonbonded pdb=" O ASP A 959 " pdb=" OG1 THR A 962 " model vdw 2.253 3.040 ... (remaining 106442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.930 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14014 Z= 0.323 Angle : 1.066 9.586 19038 Z= 0.610 Chirality : 0.055 0.269 2220 Planarity : 0.007 0.054 2358 Dihedral : 10.065 79.240 5034 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00684 (14004) covalent geometry : angle 1.05833 (19014) SS BOND : bond 0.00271 ( 6) SS BOND : angle 2.02762 ( 12) hydrogen bonds : bond 0.30990 ( 612) hydrogen bonds : angle 9.80928 ( 1764) link_NAG-ASN : bond 0.00530 ( 4) link_NAG-ASN : angle 5.00976 ( 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 : 0.492 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: 0.1290 time to fit residues: 71.0538 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 : 0.508 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 513 GLN A 596 GLN A 658 ASN A 680 HIS A 751 HIS A 933 HIS A 966 HIS ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 513 GLN B 596 GLN B 658 ASN B 680 HIS B 751 HIS B 933 HIS B 966 HIS ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.099345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085862 restraints weight = 55008.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.087709 restraints weight = 31849.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088944 restraints weight = 21765.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.089573 restraints weight = 16746.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.090289 restraints weight = 14200.713| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14014 Z= 0.189 Angle : 0.744 8.957 19038 Z= 0.388 Chirality : 0.045 0.175 2220 Planarity : 0.005 0.036 2358 Dihedral : 6.541 59.844 1960 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.06 % Allowed : 11.29 % Favored : 85.65 % 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: -3.10 (0.17), residues: 1752 helix: -1.52 (0.14), residues: 954 sheet: -1.11 (0.41), residues: 140 loop : -2.95 (0.21), 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 0.034 0.002 PHE A 538 TRP 0.020 0.002 TRP B 406 HIS 0.011 0.002 HIS A 966 Details of bonding type rmsd covalent geometry : bond 0.00417 (14004) covalent geometry : angle 0.72661 (19014) SS BOND : bond 0.00507 ( 6) SS BOND : angle 4.91051 ( 12) hydrogen bonds : bond 0.05185 ( 612) hydrogen bonds : angle 5.24844 ( 1764) link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 4.17269 ( 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 292 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.703 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: 0.8392 (OUTLIER) cc_final: 0.8099 (mt) REVERT: A 655 LEU cc_start: 0.9285 (tp) cc_final: 0.9008 (tp) REVERT: A 695 MET cc_start: 0.8292 (mtp) cc_final: 0.8046 (mtp) REVERT: B 532 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8096 (mt) REVERT: B 655 LEU cc_start: 0.9291 (tp) cc_final: 0.9006 (tp) REVERT: B 695 MET cc_start: 0.8286 (mtp) cc_final: 0.8049 (mtp) REVERT: B 712 MET cc_start: 0.7239 (ppp) cc_final: 0.7031 (ttt) REVERT: B 924 MET cc_start: 0.8612 (mmm) cc_final: 0.8395 (mpp) outliers start: 45 outliers final: 14 residues processed: 277 average time/residue: 0.0952 time to fit residues: 41.8807 Evaluate side-chains 208 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 327 VAL 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: 5.9990 chunk 19 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 66 optimal weight: 0.0980 chunk 162 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 156 optimal weight: 0.0870 overall best weight: 2.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.100304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.086928 restraints weight = 55129.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.088719 restraints weight = 32282.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.089981 restraints weight = 22291.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090838 restraints weight = 17064.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.091363 restraints weight = 14118.227| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 14014 Z= 0.174 Angle : 0.739 13.888 19038 Z= 0.371 Chirality : 0.045 0.386 2220 Planarity : 0.004 0.028 2358 Dihedral : 6.234 55.925 1960 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.79 % Allowed : 12.59 % Favored : 84.63 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.19 (0.19), residues: 1752 helix: -0.70 (0.16), residues: 956 sheet: -0.88 (0.42), residues: 140 loop : -2.66 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1139 TYR 0.020 0.002 TYR B 253 PHE 0.025 0.002 PHE A 538 TRP 0.018 0.001 TRP A 915 HIS 0.006 0.001 HIS A 770 Details of bonding type rmsd covalent geometry : bond 0.00412 (14004) covalent geometry : angle 0.72264 (19014) SS BOND : bond 0.00263 ( 6) SS BOND : angle 5.10332 ( 12) hydrogen bonds : bond 0.04519 ( 612) hydrogen bonds : angle 5.10227 ( 1764) link_NAG-ASN : bond 0.00136 ( 4) link_NAG-ASN : angle 3.69472 ( 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 261 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 655 LEU cc_start: 0.9176 (tp) cc_final: 0.8932 (tp) REVERT: A 1084 MET cc_start: 0.5732 (mmt) cc_final: 0.5266 (tpp) REVERT: B 532 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 655 LEU cc_start: 0.9188 (tp) cc_final: 0.8945 (tp) REVERT: B 712 MET cc_start: 0.7382 (ppp) cc_final: 0.6950 (tmm) REVERT: B 1084 MET cc_start: 0.5725 (mmt) cc_final: 0.5193 (tpp) outliers start: 41 outliers final: 19 residues processed: 249 average time/residue: 0.0905 time to fit residues: 35.9051 Evaluate side-chains 212 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU 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 389 VAL 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 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: 9.9990 chunk 86 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 0.0870 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN A 534 ASN A 918 HIS B 244 ASN B 534 ASN B 918 HIS B1107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.101130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087870 restraints weight = 54628.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.089767 restraints weight = 31216.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091040 restraints weight = 21080.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091843 restraints weight = 15929.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.092534 restraints weight = 13215.615| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 14014 Z= 0.136 Angle : 0.685 12.370 19038 Z= 0.336 Chirality : 0.043 0.298 2220 Planarity : 0.004 0.036 2358 Dihedral : 5.758 45.151 1960 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.40 % Allowed : 13.95 % Favored : 82.65 % 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: -1.70 (0.19), residues: 1752 helix: -0.23 (0.16), residues: 958 sheet: -0.67 (0.43), residues: 140 loop : -2.56 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 968 TYR 0.015 0.002 TYR A 965 PHE 0.019 0.001 PHE A 538 TRP 0.013 0.001 TRP A 915 HIS 0.005 0.001 HIS A 841 Details of bonding type rmsd covalent geometry : bond 0.00322 (14004) covalent geometry : angle 0.66694 (19014) SS BOND : bond 0.00496 ( 6) SS BOND : angle 5.34039 ( 12) hydrogen bonds : bond 0.03717 ( 612) hydrogen bonds : angle 4.84477 ( 1764) link_NAG-ASN : bond 0.00146 ( 4) link_NAG-ASN : angle 3.37262 ( 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 269 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 PHE cc_start: 0.7104 (t80) cc_final: 0.6869 (t80) REVERT: A 532 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8178 (mt) REVERT: A 655 LEU cc_start: 0.9084 (tp) cc_final: 0.8872 (tp) REVERT: A 1084 MET cc_start: 0.5578 (mmt) cc_final: 0.5280 (tpp) REVERT: B 532 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8178 (mt) REVERT: B 655 LEU cc_start: 0.9105 (tp) cc_final: 0.8886 (tp) REVERT: B 712 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6901 (tmm) REVERT: B 1084 MET cc_start: 0.5588 (mmt) cc_final: 0.5257 (tpp) outliers start: 50 outliers final: 27 residues processed: 252 average time/residue: 0.0931 time to fit residues: 37.9767 Evaluate side-chains 227 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 328 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 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 795 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 326 LEU Chi-restraints excluded: chain B residue 328 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 534 ASN Chi-restraints excluded: chain B residue 712 MET 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: 8.9990 chunk 21 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 0.0270 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN B 513 GLN B 534 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.100719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.087435 restraints weight = 55783.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.089234 restraints weight = 32821.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.090492 restraints weight = 22577.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.091393 restraints weight = 17287.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.091875 restraints weight = 14214.742| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 14014 Z= 0.148 Angle : 0.666 10.042 19038 Z= 0.329 Chirality : 0.043 0.267 2220 Planarity : 0.004 0.039 2358 Dihedral : 5.336 29.535 1960 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.95 % Allowed : 14.35 % Favored : 81.70 % 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: -1.47 (0.19), residues: 1752 helix: 0.02 (0.16), residues: 952 sheet: -0.54 (0.44), residues: 136 loop : -2.55 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 968 TYR 0.011 0.001 TYR A 273 PHE 0.020 0.001 PHE A 538 TRP 0.013 0.001 TRP A 570 HIS 0.004 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00351 (14004) covalent geometry : angle 0.64956 (19014) SS BOND : bond 0.00373 ( 6) SS BOND : angle 4.90998 ( 12) hydrogen bonds : bond 0.03534 ( 612) hydrogen bonds : angle 4.78167 ( 1764) link_NAG-ASN : bond 0.00161 ( 4) link_NAG-ASN : angle 3.32409 ( 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 275 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.534 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: 0.8414 (OUTLIER) cc_final: 0.8134 (mt) REVERT: A 651 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8174 (tp) REVERT: A 655 LEU cc_start: 0.9073 (tp) cc_final: 0.8827 (tp) REVERT: A 1084 MET cc_start: 0.5499 (mmt) cc_final: 0.5272 (tpp) REVERT: B 532 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (mt) REVERT: B 655 LEU cc_start: 0.9010 (tp) cc_final: 0.8795 (tp) REVERT: B 712 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6891 (tmm) REVERT: B 1084 MET cc_start: 0.5545 (mmt) cc_final: 0.5312 (tpp) outliers start: 58 outliers final: 31 residues processed: 258 average time/residue: 0.0966 time to fit residues: 39.6301 Evaluate side-chains 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 651 LEU 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 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 529 PHE 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 712 MET 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: 0.9990 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 534 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.102400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.089039 restraints weight = 54861.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090900 restraints weight = 31719.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092150 restraints weight = 21599.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.093089 restraints weight = 16514.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.093568 restraints weight = 13591.719| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14014 Z= 0.114 Angle : 0.662 9.965 19038 Z= 0.320 Chirality : 0.044 0.261 2220 Planarity : 0.004 0.042 2358 Dihedral : 5.008 29.793 1960 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.13 % Allowed : 15.85 % Favored : 81.02 % 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: -1.22 (0.19), residues: 1752 helix: 0.27 (0.17), residues: 952 sheet: -0.27 (0.45), residues: 136 loop : -2.55 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 990 TYR 0.010 0.001 TYR A 253 PHE 0.020 0.001 PHE A 538 TRP 0.013 0.001 TRP B 873 HIS 0.006 0.001 HIS A 918 Details of bonding type rmsd covalent geometry : bond 0.00261 (14004) covalent geometry : angle 0.65250 (19014) SS BOND : bond 0.00427 ( 6) SS BOND : angle 3.51899 ( 12) hydrogen bonds : bond 0.03318 ( 612) hydrogen bonds : angle 4.61120 ( 1764) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 2.99095 ( 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 260 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.518 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: 0.8407 (OUTLIER) cc_final: 0.8153 (mt) REVERT: A 695 MET cc_start: 0.8310 (mtp) cc_final: 0.8106 (mtp) REVERT: B 532 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 655 LEU cc_start: 0.8989 (tp) cc_final: 0.8744 (tp) REVERT: B 695 MET cc_start: 0.8254 (mtp) cc_final: 0.7929 (mtp) REVERT: B 712 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6815 (tmm) REVERT: B 924 MET cc_start: 0.8380 (mmm) cc_final: 0.8121 (mpp) outliers start: 46 outliers final: 25 residues processed: 241 average time/residue: 0.0984 time to fit residues: 37.3712 Evaluate side-chains 222 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 513 GLN Chi-restraints excluded: chain B residue 529 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 62 optimal weight: 0.0870 chunk 27 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 87 optimal weight: 0.0980 chunk 115 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.102388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.089010 restraints weight = 54932.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090885 restraints weight = 31966.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.092169 restraints weight = 21936.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.092854 restraints weight = 16852.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093578 restraints weight = 14225.606| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 14014 Z= 0.116 Angle : 0.665 9.730 19038 Z= 0.319 Chirality : 0.043 0.296 2220 Planarity : 0.004 0.041 2358 Dihedral : 4.828 30.427 1960 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.65 % Allowed : 17.48 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.20), residues: 1752 helix: 0.43 (0.17), residues: 954 sheet: -0.23 (0.45), residues: 136 loop : -2.41 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.009 0.001 TYR A 253 PHE 0.015 0.001 PHE B 650 TRP 0.013 0.001 TRP A 873 HIS 0.004 0.001 HIS B 816 Details of bonding type rmsd covalent geometry : bond 0.00271 (14004) covalent geometry : angle 0.65615 (19014) SS BOND : bond 0.00472 ( 6) SS BOND : angle 3.31673 ( 12) hydrogen bonds : bond 0.03351 ( 612) hydrogen bonds : angle 4.48546 ( 1764) link_NAG-ASN : bond 0.00160 ( 4) link_NAG-ASN : angle 2.81928 ( 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 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 532 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8165 (mt) REVERT: B 655 LEU cc_start: 0.9033 (tp) cc_final: 0.8757 (tp) REVERT: B 712 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6833 (tmm) outliers start: 39 outliers final: 31 residues processed: 219 average time/residue: 0.0892 time to fit residues: 31.8910 Evaluate side-chains 220 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 488 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 692 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 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 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 692 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.100103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086581 restraints weight = 56000.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.088381 restraints weight = 33469.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.089556 restraints weight = 23362.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.090262 restraints weight = 18304.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090889 restraints weight = 15568.172| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 14014 Z= 0.181 Angle : 0.743 11.807 19038 Z= 0.362 Chirality : 0.045 0.292 2220 Planarity : 0.004 0.044 2358 Dihedral : 5.058 30.452 1960 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.61 % Allowed : 17.82 % Favored : 78.57 % 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: -1.12 (0.19), residues: 1752 helix: 0.38 (0.17), residues: 936 sheet: -0.50 (0.44), residues: 136 loop : -2.43 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1113 TYR 0.011 0.001 TYR A 253 PHE 0.018 0.002 PHE B 347 TRP 0.011 0.002 TRP B 570 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00422 (14004) covalent geometry : angle 0.72533 (19014) SS BOND : bond 0.00524 ( 6) SS BOND : angle 5.67811 ( 12) hydrogen bonds : bond 0.03764 ( 612) hydrogen bonds : angle 4.84451 ( 1764) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 3.21090 ( 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 248 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.518 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: A 532 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 695 MET cc_start: 0.8241 (mtp) cc_final: 0.8008 (mpp) REVERT: A 707 MET cc_start: 0.7219 (mmm) cc_final: 0.6998 (mmt) REVERT: B 532 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8103 (mp) REVERT: B 692 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7752 (tt) REVERT: B 707 MET cc_start: 0.7674 (mmp) cc_final: 0.7177 (mmt) REVERT: B 712 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6948 (tmm) REVERT: B 924 MET cc_start: 0.8327 (mmm) cc_final: 0.8032 (mpp) outliers start: 53 outliers final: 41 residues processed: 231 average time/residue: 0.0818 time to fit residues: 30.5573 Evaluate side-chains 236 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 488 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 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 348 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 846 CYS Chi-restraints excluded: chain B residue 873 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 111 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 63 optimal weight: 0.0980 chunk 71 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.101224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.087969 restraints weight = 54938.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.089823 restraints weight = 32109.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.091018 restraints weight = 22036.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.091827 restraints weight = 16973.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.092432 restraints weight = 14159.124| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 14014 Z= 0.136 Angle : 0.710 10.174 19038 Z= 0.341 Chirality : 0.046 0.311 2220 Planarity : 0.004 0.047 2358 Dihedral : 4.949 29.614 1960 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.99 % Allowed : 18.44 % Favored : 78.57 % 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: -1.04 (0.20), residues: 1752 helix: 0.44 (0.17), residues: 940 sheet: -0.55 (0.44), residues: 136 loop : -2.38 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 881 TYR 0.009 0.001 TYR B 253 PHE 0.014 0.001 PHE A 347 TRP 0.014 0.001 TRP A 873 HIS 0.007 0.001 HIS B 918 Details of bonding type rmsd covalent geometry : bond 0.00325 (14004) covalent geometry : angle 0.69585 (19014) SS BOND : bond 0.00420 ( 6) SS BOND : angle 4.83348 ( 12) hydrogen bonds : bond 0.03536 ( 612) hydrogen bonds : angle 4.77677 ( 1764) link_NAG-ASN : bond 0.00107 ( 4) link_NAG-ASN : angle 3.02080 ( 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 241 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.493 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 451 TYR cc_start: 0.7088 (m-80) cc_final: 0.6734 (m-10) REVERT: A 532 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8049 (mp) REVERT: B 451 TYR cc_start: 0.7104 (m-80) cc_final: 0.6741 (m-10) REVERT: B 532 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8024 (mp) REVERT: B 707 MET cc_start: 0.7047 (mmp) cc_final: 0.6841 (mmt) REVERT: B 712 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6924 (tmm) REVERT: B 924 MET cc_start: 0.8359 (mmm) cc_final: 0.8039 (mpp) outliers start: 44 outliers final: 33 residues processed: 226 average time/residue: 0.0865 time to fit residues: 31.7050 Evaluate side-chains 226 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU 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 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 482 THR Chi-restraints excluded: chain B residue 488 LEU 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 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: 2.9990 chunk 124 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 0.0000 chunk 120 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.102550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.089308 restraints weight = 54217.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091201 restraints weight = 31464.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.092502 restraints weight = 21503.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.093348 restraints weight = 16414.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.093941 restraints weight = 13589.623| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14014 Z= 0.121 Angle : 0.726 11.170 19038 Z= 0.344 Chirality : 0.045 0.314 2220 Planarity : 0.004 0.046 2358 Dihedral : 4.780 31.450 1960 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.38 % Allowed : 19.59 % 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: -0.93 (0.20), residues: 1752 helix: 0.58 (0.17), residues: 938 sheet: -0.52 (0.45), residues: 136 loop : -2.40 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.015 0.001 TYR B 283 PHE 0.011 0.001 PHE B1124 TRP 0.016 0.001 TRP A 873 HIS 0.008 0.001 HIS B 841 Details of bonding type rmsd covalent geometry : bond 0.00271 (14004) covalent geometry : angle 0.71921 (19014) SS BOND : bond 0.00427 ( 6) SS BOND : angle 3.09220 ( 12) hydrogen bonds : bond 0.03526 ( 612) hydrogen bonds : angle 4.67641 ( 1764) link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 2.71887 ( 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 244 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.530 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: 0.8397 (OUTLIER) cc_final: 0.8149 (mt) REVERT: B 532 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 704 ILE cc_start: 0.7976 (mm) cc_final: 0.7709 (mm) REVERT: B 712 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6922 (tmm) outliers start: 35 outliers final: 27 residues processed: 236 average time/residue: 0.0910 time to fit residues: 34.2719 Evaluate side-chains 226 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 488 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 945 THR 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 488 LEU 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: 8.9990 chunk 104 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN ** 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 = 0.3970 r_free = 0.3970 target = 0.101663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.088476 restraints weight = 55530.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.090330 restraints weight = 33060.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.091633 restraints weight = 22883.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.092384 restraints weight = 17543.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.093000 restraints weight = 14698.031| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14014 Z= 0.130 Angle : 0.735 10.852 19038 Z= 0.347 Chirality : 0.046 0.315 2220 Planarity : 0.004 0.045 2358 Dihedral : 4.724 29.941 1960 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.65 % Allowed : 19.12 % Favored : 78.23 % 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: 0.62 (0.17), residues: 940 sheet: -0.60 (0.45), residues: 136 loop : -2.36 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 881 TYR 0.011 0.001 TYR A 253 PHE 0.031 0.001 PHE B 963 TRP 0.014 0.001 TRP A 873 HIS 0.008 0.001 HIS B 841 Details of bonding type rmsd covalent geometry : bond 0.00298 (14004) covalent geometry : angle 0.73063 (19014) SS BOND : bond 0.00379 ( 6) SS BOND : angle 1.71015 ( 12) hydrogen bonds : bond 0.03445 ( 612) hydrogen bonds : angle 4.66823 ( 1764) link_NAG-ASN : bond 0.00114 ( 4) link_NAG-ASN : angle 2.79850 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2257.59 seconds wall clock time: 39 minutes 46.74 seconds (2386.74 seconds total)