Starting phenix.real_space_refine on Thu Sep 26 17:46:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/09_2024/7d90_30616.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/09_2024/7d90_30616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/09_2024/7d90_30616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/09_2024/7d90_30616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/09_2024/7d90_30616.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d90_30616/09_2024/7d90_30616.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 8910 2.51 5 N 2266 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13686 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6815 Classifications: {'peptide': 880} Link IDs: {'PTRANS': 32, 'TRANS': 847} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B Time building chain proxies: 15.20, per 1000 atoms: 1.11 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=3, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1201 " - " ASN A 379 " " NAG A1202 " - " ASN A 428 " " NAG B1201 " - " ASN B 379 " " NAG B1202 " - " ASN B 428 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 59.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 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: 4.76 Time building geometry restraints manager: 3.82 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: 7800 15.85 - 31.70: 399 31.70 - 47.54: 73 47.54 - 63.39: 7 63.39 - 79.24: 4 Dihedral angle restraints: 8283 sinusoidal: 3237 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=" 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 dihedral pdb=" CA SER B 471 " pdb=" C SER B 471 " pdb=" N LEU B 472 " pdb=" CA LEU B 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 8280 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: 2.03 - 2.60: 133 2.60 - 3.18: 11722 3.18 - 3.75: 20847 3.75 - 4.33: 28568 4.33 - 4.90: 45186 Nonbonded interactions: 106456 Sorted by model distance: nonbonded pdb=" SG CYS B 410 " pdb=" SG CYS B 420 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 271 " pdb=" SG CYS B 653 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS B 375 " pdb=" SG CYS B 390 " model vdw 2.029 3.760 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 ... (remaining 106451 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 40.060 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- 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 14004 Z= 0.448 Angle : 1.058 9.586 19014 Z= 0.608 Chirality : 0.055 0.269 2220 Planarity : 0.007 0.054 2358 Dihedral : 10.065 79.240 5034 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.14 % Allowed : 2.59 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.00 (0.15), residues: 1752 helix: -3.77 (0.10), residues: 870 sheet: -1.42 (0.44), residues: 126 loop : -2.94 (0.18), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 406 HIS 0.012 0.003 HIS B 841 PHE 0.036 0.003 PHE B 826 TYR 0.014 0.003 TYR A 701 ARG 0.015 0.001 ARG A 968 *********************** 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 fitting. rotamer outliers: 2 poor density : 386 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8631 (mm) cc_final: 0.8399 (tp) REVERT: A 314 MET cc_start: 0.8494 (tpt) cc_final: 0.8277 (tpt) REVERT: A 469 LEU cc_start: 0.7369 (tp) cc_final: 0.7041 (mp) REVERT: A 532 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 292 LEU cc_start: 0.8621 (mm) cc_final: 0.8387 (tp) REVERT: B 314 MET cc_start: 0.8483 (tpt) cc_final: 0.8264 (tpt) REVERT: B 469 LEU cc_start: 0.7362 (tp) cc_final: 0.7028 (mp) REVERT: B 532 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8025 (mt) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.2691 time to fit residues: 147.1520 Evaluate side-chains 215 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain B residue 532 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS A 513 GLN A 596 GLN A 658 ASN A 680 HIS A 751 HIS A 933 HIS A 966 HIS ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS B 513 GLN B 596 GLN B 658 ASN B 680 HIS B 751 HIS B 933 HIS B 966 HIS ** B1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14004 Z= 0.266 Angle : 0.717 9.234 19014 Z= 0.375 Chirality : 0.044 0.174 2220 Planarity : 0.005 0.037 2358 Dihedral : 6.493 59.838 1960 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.27 % Allowed : 11.50 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.17), residues: 1752 helix: -1.51 (0.14), residues: 954 sheet: -1.15 (0.40), residues: 140 loop : -2.94 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 406 HIS 0.011 0.002 HIS A 966 PHE 0.031 0.002 PHE A 538 TYR 0.015 0.002 TYR A 273 ARG 0.006 0.001 ARG B 675 *********************** 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 290 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 242 time to evaluate : 1.708 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: 0.8339 (OUTLIER) cc_final: 0.8039 (mt) REVERT: A 655 LEU cc_start: 0.9248 (tp) cc_final: 0.9016 (tp) REVERT: A 695 MET cc_start: 0.8339 (mtp) cc_final: 0.8025 (mtp) REVERT: A 712 MET cc_start: 0.7319 (ppp) cc_final: 0.7108 (ttt) REVERT: A 817 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 376 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6212 (mmm) REVERT: B 532 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8042 (mt) REVERT: B 695 MET cc_start: 0.8351 (mtp) cc_final: 0.8098 (mtp) REVERT: B 712 MET cc_start: 0.7314 (ppp) cc_final: 0.7104 (ttt) outliers start: 48 outliers final: 12 residues processed: 272 average time/residue: 0.2209 time to fit residues: 93.0457 Evaluate side-chains 215 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 817 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 268 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 88 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 14004 Z= 0.250 Angle : 0.701 9.491 19014 Z= 0.349 Chirality : 0.044 0.250 2220 Planarity : 0.004 0.030 2358 Dihedral : 6.140 56.669 1960 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.40 % Allowed : 12.86 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1752 helix: -0.66 (0.16), residues: 956 sheet: -0.93 (0.42), residues: 140 loop : -2.71 (0.21), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 915 HIS 0.005 0.001 HIS A 770 PHE 0.026 0.002 PHE A 538 TYR 0.021 0.002 TYR B 253 ARG 0.005 0.000 ARG B 675 *********************** 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 269 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8094 (mt) REVERT: A 655 LEU cc_start: 0.9124 (tp) cc_final: 0.8869 (tp) REVERT: A 695 MET cc_start: 0.8306 (mtp) cc_final: 0.8078 (mtp) REVERT: A 712 MET cc_start: 0.7437 (ppp) cc_final: 0.6844 (ttt) REVERT: A 1084 MET cc_start: 0.5843 (mmt) cc_final: 0.5298 (tpp) REVERT: B 532 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8099 (mt) REVERT: B 655 LEU cc_start: 0.9265 (tp) cc_final: 0.9007 (tp) REVERT: B 712 MET cc_start: 0.7447 (ppp) cc_final: 0.6853 (ttt) REVERT: B 1084 MET cc_start: 0.5954 (mmt) cc_final: 0.5378 (tpp) outliers start: 50 outliers final: 22 residues processed: 252 average time/residue: 0.2117 time to fit residues: 82.5177 Evaluate side-chains 221 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 1.445 ------------------------------------------------------------------------------- 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 340 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 1135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 141 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 HIS ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS B1107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14004 Z= 0.272 Angle : 0.698 8.154 19014 Z= 0.349 Chirality : 0.044 0.289 2220 Planarity : 0.004 0.036 2358 Dihedral : 5.723 35.491 1960 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.08 % Allowed : 13.40 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1752 helix: -0.22 (0.16), residues: 954 sheet: -0.72 (0.42), residues: 138 loop : -2.70 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 915 HIS 0.006 0.002 HIS A 426 PHE 0.017 0.002 PHE A 538 TYR 0.015 0.002 TYR B 965 ARG 0.003 0.000 ARG A 675 *********************** 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 264 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 204 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 695 MET cc_start: 0.8361 (mtp) cc_final: 0.8083 (mtp) REVERT: A 712 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6951 (tmm) REVERT: A 841 HIS cc_start: 0.7276 (t-90) cc_final: 0.6765 (t-90) REVERT: A 1084 MET cc_start: 0.5809 (mmt) cc_final: 0.5383 (tpp) REVERT: B 268 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7798 (p) REVERT: B 532 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 695 MET cc_start: 0.8328 (mtp) cc_final: 0.8034 (mpp) REVERT: B 712 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6986 (tmm) REVERT: B 817 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7518 (mt) REVERT: B 1084 MET cc_start: 0.5813 (mmt) cc_final: 0.5379 (tpp) outliers start: 60 outliers final: 37 residues processed: 240 average time/residue: 0.2006 time to fit residues: 75.9395 Evaluate side-chains 232 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 328 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 560 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 328 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 389 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 14004 Z= 0.254 Angle : 0.682 11.726 19014 Z= 0.340 Chirality : 0.044 0.291 2220 Planarity : 0.004 0.039 2358 Dihedral : 5.369 29.709 1960 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.35 % Allowed : 14.76 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1752 helix: 0.05 (0.17), residues: 938 sheet: -0.76 (0.42), residues: 138 loop : -2.64 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 570 HIS 0.005 0.001 HIS B 426 PHE 0.022 0.002 PHE A 650 TYR 0.016 0.001 TYR B 965 ARG 0.002 0.000 ARG B 675 *********************** 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 278 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 214 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 712 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6954 (tmm) REVERT: A 1084 MET cc_start: 0.5650 (mmt) cc_final: 0.5364 (tpp) REVERT: B 268 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7829 (p) REVERT: B 532 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 695 MET cc_start: 0.8357 (mtp) cc_final: 0.8053 (mtp) REVERT: B 712 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6987 (tmm) REVERT: B 1084 MET cc_start: 0.5674 (mmt) cc_final: 0.5347 (tpp) outliers start: 64 outliers final: 35 residues processed: 259 average time/residue: 0.2015 time to fit residues: 81.6825 Evaluate side-chains 235 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 839 ILE 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 153 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14004 Z= 0.220 Angle : 0.683 10.728 19014 Z= 0.334 Chirality : 0.044 0.307 2220 Planarity : 0.004 0.041 2358 Dihedral : 5.234 30.027 1960 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 4.69 % Allowed : 15.03 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1752 helix: 0.24 (0.17), residues: 936 sheet: -0.60 (0.43), residues: 138 loop : -2.62 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 570 HIS 0.007 0.001 HIS B 918 PHE 0.017 0.001 PHE A 538 TYR 0.010 0.001 TYR B 701 ARG 0.003 0.000 ARG A 881 *********************** 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 278 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 209 time to evaluate : 1.881 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: 0.8379 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 712 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6945 (tmm) REVERT: A 1084 MET cc_start: 0.5603 (mmt) cc_final: 0.5373 (tpp) REVERT: B 268 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7741 (p) REVERT: B 532 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 695 MET cc_start: 0.8448 (mtp) cc_final: 0.8225 (mtp) REVERT: B 712 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6945 (tmm) REVERT: B 1084 MET cc_start: 0.5592 (mmt) cc_final: 0.5313 (tpp) outliers start: 69 outliers final: 45 residues processed: 255 average time/residue: 0.2208 time to fit residues: 86.3494 Evaluate side-chains 246 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 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 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 839 ILE Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 106 optimal weight: 0.0970 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 918 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 14004 Z= 0.216 Angle : 0.679 10.264 19014 Z= 0.330 Chirality : 0.044 0.309 2220 Planarity : 0.004 0.043 2358 Dihedral : 5.124 30.161 1960 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.95 % Allowed : 16.46 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.19), residues: 1752 helix: 0.30 (0.16), residues: 956 sheet: -0.52 (0.43), residues: 138 loop : -2.57 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 873 HIS 0.006 0.001 HIS A 918 PHE 0.018 0.001 PHE B 538 TYR 0.010 0.001 TYR B 253 ARG 0.002 0.000 ARG B 675 *********************** 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 267 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 209 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.7150 (m-80) cc_final: 0.6734 (m-10) REVERT: A 532 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 712 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6964 (tmm) REVERT: B 268 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.7908 (p) REVERT: B 451 TYR cc_start: 0.7145 (m-80) cc_final: 0.6726 (m-10) REVERT: B 532 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7961 (mp) REVERT: B 712 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6962 (tmm) outliers start: 58 outliers final: 39 residues processed: 242 average time/residue: 0.2096 time to fit residues: 79.6939 Evaluate side-chains 239 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 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 529 PHE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 0.0030 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 154 optimal weight: 0.9980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14004 Z= 0.182 Angle : 0.678 10.477 19014 Z= 0.326 Chirality : 0.044 0.326 2220 Planarity : 0.004 0.046 2358 Dihedral : 4.886 30.352 1960 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.99 % Allowed : 18.50 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1752 helix: 0.48 (0.17), residues: 952 sheet: -0.39 (0.43), residues: 138 loop : -2.41 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 873 HIS 0.005 0.001 HIS A 816 PHE 0.019 0.001 PHE B 538 TYR 0.011 0.001 TYR B 283 ARG 0.003 0.000 ARG B 881 *********************** 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 260 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 1.599 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 292 LEU cc_start: 0.8647 (tt) cc_final: 0.8395 (tp) REVERT: A 451 TYR cc_start: 0.7138 (m-80) cc_final: 0.6768 (m-10) REVERT: A 532 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7919 (mp) REVERT: A 712 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6862 (tmm) REVERT: A 1084 MET cc_start: 0.7678 (tpp) cc_final: 0.7112 (mmt) REVERT: B 451 TYR cc_start: 0.7093 (m-80) cc_final: 0.6746 (m-10) REVERT: B 532 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 712 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6880 (tmm) REVERT: B 1084 MET cc_start: 0.7630 (tpp) cc_final: 0.7056 (mmt) outliers start: 44 outliers final: 30 residues processed: 244 average time/residue: 0.2104 time to fit residues: 80.4779 Evaluate side-chains 234 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 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 482 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 873 TRP Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 236 ILE 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 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 532 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 829 LEU 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 162 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 68 optimal weight: 30.0000 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 149 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14004 Z= 0.207 Angle : 0.691 10.997 19014 Z= 0.332 Chirality : 0.045 0.320 2220 Planarity : 0.004 0.047 2358 Dihedral : 4.867 30.245 1960 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.99 % Allowed : 18.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1752 helix: 0.51 (0.17), residues: 950 sheet: -0.39 (0.43), residues: 138 loop : -2.42 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 873 HIS 0.006 0.001 HIS B 841 PHE 0.031 0.001 PHE A 963 TYR 0.011 0.001 TYR B 283 ARG 0.002 0.000 ARG B 675 *********************** 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 252 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 208 time to evaluate : 1.569 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 292 LEU cc_start: 0.8650 (tt) cc_final: 0.8410 (tp) REVERT: A 451 TYR cc_start: 0.7137 (m-80) cc_final: 0.6848 (m-10) REVERT: A 532 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7940 (mp) REVERT: A 695 MET cc_start: 0.8136 (mpp) cc_final: 0.7874 (mpp) REVERT: A 712 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6880 (tmm) REVERT: B 451 TYR cc_start: 0.7138 (m-80) cc_final: 0.6844 (m-10) REVERT: B 532 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7943 (mp) REVERT: B 712 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6885 (tmm) outliers start: 44 outliers final: 35 residues processed: 241 average time/residue: 0.2130 time to fit residues: 79.4754 Evaluate side-chains 239 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 208 LEU 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 358 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 797 VAL Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 8.9990 chunk 102 optimal weight: 0.0000 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 40.0000 chunk 175 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14004 Z= 0.188 Angle : 0.702 10.870 19014 Z= 0.334 Chirality : 0.045 0.330 2220 Planarity : 0.004 0.046 2358 Dihedral : 4.796 30.215 1960 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.93 % Allowed : 19.39 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1752 helix: 0.57 (0.17), residues: 950 sheet: -0.41 (0.43), residues: 138 loop : -2.43 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 873 HIS 0.009 0.001 HIS B 841 PHE 0.039 0.001 PHE B 685 TYR 0.009 0.001 TYR B 283 ARG 0.002 0.000 ARG A1082 ********************** 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 250 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 704 ILE cc_start: 0.8234 (mm) cc_final: 0.8026 (mm) REVERT: A 712 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6955 (tmm) REVERT: B 451 TYR cc_start: 0.6968 (m-80) cc_final: 0.6767 (m-10) REVERT: B 532 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7929 (mp) REVERT: B 712 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6882 (tmm) outliers start: 43 outliers final: 35 residues processed: 240 average time/residue: 0.2101 time to fit residues: 78.4323 Evaluate side-chains 235 residues out of total 1470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 348 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 405 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 712 MET Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1090 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 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 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 532 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 873 TRP Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 918 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN B 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.101125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.088110 restraints weight = 55283.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.089902 restraints weight = 32893.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.091142 restraints weight = 22816.141| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 14004 Z= 0.212 Angle : 0.718 11.232 19014 Z= 0.342 Chirality : 0.045 0.321 2220 Planarity : 0.004 0.048 2358 Dihedral : 4.792 30.098 1960 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.99 % Allowed : 19.46 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1752 helix: 0.60 (0.17), residues: 948 sheet: -0.40 (0.44), residues: 138 loop : -2.42 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 873 HIS 0.010 0.001 HIS B 841 PHE 0.023 0.001 PHE A 685 TYR 0.010 0.001 TYR B 253 ARG 0.002 0.000 ARG B1082 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2698.95 seconds wall clock time: 49 minutes 4.78 seconds (2944.78 seconds total)