Starting phenix.real_space_refine on Wed Mar 4 11:04:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n3n_24141/03_2026/7n3n_24141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n3n_24141/03_2026/7n3n_24141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n3n_24141/03_2026/7n3n_24141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n3n_24141/03_2026/7n3n_24141.map" model { file = "/net/cci-nas-00/data/ceres_data/7n3n_24141/03_2026/7n3n_24141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n3n_24141/03_2026/7n3n_24141.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.070 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: 5 Type Number sf(0) Gaussians S 82 5.16 5 Cl 2 4.86 5 C 8495 2.51 5 N 2140 2.21 5 O 2307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6487 Classifications: {'peptide': 832} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 802} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 6497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6497 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 29, 'TRANS': 801} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'FUN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.30, per 1000 atoms: 0.25 Number of scatterers: 13026 At special positions: 0 Unit cell: (81.32, 155.15, 115.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 82 16.00 O 2307 8.00 N 2140 7.00 C 8495 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " 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 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 427.5 milliseconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3080 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 4 sheets defined 62.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.372A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.502A pdb=" N SER A 320 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.067A pdb=" N LEU A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 399 removed outlier: 4.354A pdb=" N GLY A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 Processing helix chain 'A' and resid 428 through 453 removed outlier: 4.405A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 440 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 476 removed outlier: 4.084A pdb=" N PHE A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.768A pdb=" N VAL A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) Proline residue: A 496 - end of helix removed outlier: 3.531A pdb=" N THR A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.930A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 542 Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 599 through 633 removed outlier: 3.609A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 642 removed outlier: 5.454A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 667 Processing helix chain 'A' and resid 673 through 700 removed outlier: 4.192A pdb=" N ILE A 677 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.736A pdb=" N SER A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 removed outlier: 3.542A pdb=" N TYR A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 779 Processing helix chain 'A' and resid 801 through 813 removed outlier: 3.790A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 849 Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.678A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Proline residue: A1040 - end of helix removed outlier: 3.609A pdb=" N THR A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1097 through 1109 removed outlier: 3.792A pdb=" N ILE A1101 " --> pdb=" O LYS A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1130 removed outlier: 3.622A pdb=" N GLU A1130 " --> pdb=" O MET A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1191 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.941A pdb=" N VAL B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 304 removed outlier: 3.650A pdb=" N LEU B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 304' Processing helix chain 'B' and resid 305 through 315 removed outlier: 4.436A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 344 Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.806A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.626A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 454 removed outlier: 3.671A pdb=" N ALA B 434 " --> pdb=" O TRP B 430 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 removed outlier: 4.193A pdb=" N GLU B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY B 478 " --> pdb=" O ASN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 3.507A pdb=" N VAL B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 removed outlier: 4.405A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 544 removed outlier: 3.625A pdb=" N LYS B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL B 532 " --> pdb=" O ILE B 528 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY B 541 " --> pdb=" O ALA B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 removed outlier: 3.553A pdb=" N CYS B 568 " --> pdb=" O SER B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 599 through 632 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 636 through 642 removed outlier: 4.474A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 667 removed outlier: 3.928A pdb=" N LEU B 663 " --> pdb=" O PHE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 699 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 731 removed outlier: 3.658A pdb=" N ILE B 730 " --> pdb=" O VAL B 726 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN B 731 " --> pdb=" O MET B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 751 removed outlier: 3.538A pdb=" N ALA B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 779 removed outlier: 4.164A pdb=" N ASN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.858A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 849 Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.849A pdb=" N PHE B 907 " --> pdb=" O TYR B 903 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 908 " --> pdb=" O ILE B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1064 through 1079 removed outlier: 3.962A pdb=" N ASP B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1119 through 1130 Processing helix chain 'B' and resid 1136 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1191 removed outlier: 3.588A pdb=" N SER B1191 " --> pdb=" O LEU B1187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.691A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A 792 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLY A 887 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N MET A 794 " --> pdb=" O GLY A 887 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 884 " --> pdb=" O VAL A 918 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE A 920 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 886 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A1197 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A1166 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A1200 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N MET A1168 " --> pdb=" O VAL A1200 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1165 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A1054 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N MET A1087 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1112 through 1113 Processing sheet with id=AA3, first strand: chain 'B' and resid 856 through 859 removed outlier: 7.717A pdb=" N ALA B 856 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 820 " --> pdb=" O ALA B 856 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL B 858 " --> pdb=" O CYS B 820 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N HIS B 822 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLY B 887 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B1169 " --> pdb=" O TRP B1027 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B1055 " --> pdb=" O ILE B1024 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1112 through 1113 744 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2136 1.32 - 1.45: 3490 1.45 - 1.57: 7550 1.57 - 1.69: 0 1.69 - 1.82: 142 Bond restraints: 13318 Sorted by residual: bond pdb=" C4 FUN A1301 " pdb=" N2 FUN A1301 " ideal model delta sigma weight residual 1.340 1.451 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 FUN B1301 " pdb=" N2 FUN B1301 " ideal model delta sigma weight residual 1.340 1.450 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" CA ASN A 814 " pdb=" C ASN A 814 " ideal model delta sigma weight residual 1.526 1.463 0.062 1.31e-02 5.83e+03 2.26e+01 bond pdb=" CA LYS A 813 " pdb=" C LYS A 813 " ideal model delta sigma weight residual 1.524 1.477 0.046 1.27e-02 6.20e+03 1.33e+01 bond pdb=" C7 FUN B1301 " pdb=" C8 FUN B1301 " ideal model delta sigma weight residual 1.429 1.360 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 13313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 17920 3.61 - 7.22: 129 7.22 - 10.83: 13 10.83 - 14.44: 1 14.44 - 18.05: 2 Bond angle restraints: 18065 Sorted by residual: angle pdb=" N ARG A 482 " pdb=" CA ARG A 482 " pdb=" C ARG A 482 " ideal model delta sigma weight residual 111.28 121.00 -9.72 1.09e+00 8.42e-01 7.95e+01 angle pdb=" N PHE A 481 " pdb=" CA PHE A 481 " pdb=" C PHE A 481 " ideal model delta sigma weight residual 110.80 123.72 -12.92 2.13e+00 2.20e-01 3.68e+01 angle pdb=" O1 FUN B1301 " pdb=" S1 FUN B1301 " pdb=" O2 FUN B1301 " ideal model delta sigma weight residual 119.17 101.12 18.05 3.00e+00 1.11e-01 3.62e+01 angle pdb=" O1 FUN A1301 " pdb=" S1 FUN A1301 " pdb=" O2 FUN A1301 " ideal model delta sigma weight residual 119.17 101.37 17.80 3.00e+00 1.11e-01 3.52e+01 angle pdb=" N PRO A 479 " pdb=" CA PRO A 479 " pdb=" C PRO A 479 " ideal model delta sigma weight residual 113.53 119.48 -5.95 1.39e+00 5.18e-01 1.83e+01 ... (remaining 18060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7143 17.71 - 35.41: 591 35.41 - 53.12: 99 53.12 - 70.83: 24 70.83 - 88.53: 7 Dihedral angle restraints: 7864 sinusoidal: 3071 harmonic: 4793 Sorted by residual: dihedral pdb=" C PHE A 481 " pdb=" N PHE A 481 " pdb=" CA PHE A 481 " pdb=" CB PHE A 481 " ideal model delta harmonic sigma weight residual -122.60 -142.17 19.57 0 2.50e+00 1.60e-01 6.13e+01 dihedral pdb=" N PHE A 481 " pdb=" C PHE A 481 " pdb=" CA PHE A 481 " pdb=" CB PHE A 481 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.90e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual -86.00 -146.43 60.43 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2070 0.187 - 0.373: 9 0.373 - 0.560: 2 0.560 - 0.747: 0 0.747 - 0.933: 1 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA PHE A 481 " pdb=" N PHE A 481 " pdb=" C PHE A 481 " pdb=" CB PHE A 481 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" CA PHE A 811 " pdb=" N PHE A 811 " pdb=" C PHE A 811 " pdb=" CB PHE A 811 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ARG A 482 " pdb=" N ARG A 482 " pdb=" C ARG A 482 " pdb=" CB ARG A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.42e+00 ... (remaining 2079 not shown) Planarity restraints: 2243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 300 " -0.023 2.00e-02 2.50e+03 2.57e-02 1.65e+01 pdb=" CG TRP A 300 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 300 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 300 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 300 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 300 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 300 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 300 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 300 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 728 " -0.024 2.00e-02 2.50e+03 2.16e-02 8.14e+00 pdb=" CG PHE B 728 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 728 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 728 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 728 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 728 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 728 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 728 " -0.028 2.00e-02 2.50e+03 2.05e-02 7.35e+00 pdb=" CG PHE A 728 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE A 728 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 728 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 728 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 728 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 728 " -0.016 2.00e-02 2.50e+03 ... (remaining 2240 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 21 2.39 - 3.01: 7338 3.01 - 3.64: 20390 3.64 - 4.27: 29311 4.27 - 4.90: 49204 Nonbonded interactions: 106264 Sorted by model distance: nonbonded pdb=" CB PHE A 346 " pdb=" CD2 LEU A 355 " model vdw 1.756 3.860 nonbonded pdb=" O ASN A 757 " pdb=" OG1 THR A 762 " model vdw 2.173 3.040 nonbonded pdb=" O GLN B 763 " pdb=" OG1 THR B 766 " model vdw 2.215 3.040 nonbonded pdb=" O TYR A 746 " pdb=" OG1 THR A 750 " model vdw 2.226 3.040 nonbonded pdb=" O VAL B 450 " pdb=" OG1 THR B 453 " model vdw 2.228 3.040 ... (remaining 106259 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' and (resid 287 through 926 or resid 1020 through 1301)) selection = (chain 'B' and (resid 287 through 345 or (resid 346 through 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 1208 or resid 1301 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.750 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.920 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.005 0.111 13321 Z= 0.258 Angle : 0.833 18.053 18071 Z= 0.457 Chirality : 0.054 0.933 2082 Planarity : 0.006 0.063 2243 Dihedral : 13.626 88.533 4775 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.22 % Allowed : 0.57 % Favored : 99.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1655 helix: 0.40 (0.16), residues: 940 sheet: -0.87 (0.47), residues: 129 loop : -2.21 (0.21), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 898 TYR 0.024 0.002 TYR A 353 PHE 0.049 0.002 PHE B 728 TRP 0.067 0.002 TRP A 300 HIS 0.003 0.001 HIS B 773 Details of bonding type rmsd covalent geometry : bond 0.00492 (13318) covalent geometry : angle 0.83236 (18065) SS BOND : bond 0.00234 ( 3) SS BOND : angle 2.38836 ( 6) hydrogen bonds : bond 0.14448 ( 744) hydrogen bonds : angle 6.08254 ( 2205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 0.458 Fit side-chains REVERT: A 402 MET cc_start: 0.6509 (tmm) cc_final: 0.3596 (mmt) REVERT: A 590 PHE cc_start: 0.6053 (m-80) cc_final: 0.5678 (m-80) REVERT: B 748 TYR cc_start: 0.7324 (t80) cc_final: 0.7121 (t80) REVERT: B 1128 GLU cc_start: 0.6178 (pt0) cc_final: 0.5894 (pt0) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.1012 time to fit residues: 37.0527 Evaluate side-chains 198 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0060 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.0970 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.220361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169375 restraints weight = 16761.590| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.41 r_work: 0.3816 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13321 Z= 0.136 Angle : 0.594 12.686 18071 Z= 0.313 Chirality : 0.043 0.223 2082 Planarity : 0.005 0.059 2243 Dihedral : 6.516 82.692 1780 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.93 % Allowed : 7.46 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.20), residues: 1655 helix: 0.76 (0.16), residues: 977 sheet: -0.85 (0.46), residues: 129 loop : -2.15 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 482 TYR 0.038 0.001 TYR A 739 PHE 0.042 0.002 PHE B 728 TRP 0.030 0.001 TRP A 300 HIS 0.006 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00286 (13318) covalent geometry : angle 0.59255 (18065) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.99209 ( 6) hydrogen bonds : bond 0.04805 ( 744) hydrogen bonds : angle 4.78892 ( 2205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 0.471 Fit side-chains REVERT: A 402 MET cc_start: 0.5885 (tmm) cc_final: 0.3038 (mmt) REVERT: A 590 PHE cc_start: 0.6805 (m-80) cc_final: 0.6482 (m-80) REVERT: A 721 ILE cc_start: 0.8181 (mm) cc_final: 0.7907 (tp) REVERT: A 732 TRP cc_start: 0.6669 (p-90) cc_final: 0.6358 (p-90) REVERT: A 1120 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6675 (mm-40) REVERT: B 748 TYR cc_start: 0.7025 (t80) cc_final: 0.6578 (t80) outliers start: 13 outliers final: 8 residues processed: 222 average time/residue: 0.0939 time to fit residues: 33.0347 Evaluate side-chains 204 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.218693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169131 restraints weight = 16893.864| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.21 r_work: 0.3812 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13321 Z= 0.160 Angle : 0.592 13.019 18071 Z= 0.310 Chirality : 0.043 0.179 2082 Planarity : 0.005 0.059 2243 Dihedral : 6.406 84.031 1780 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.58 % Allowed : 10.75 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1655 helix: 0.84 (0.16), residues: 977 sheet: -0.98 (0.44), residues: 129 loop : -2.14 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1064 TYR 0.019 0.001 TYR A 353 PHE 0.041 0.002 PHE B 728 TRP 0.028 0.001 TRP A 300 HIS 0.006 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00366 (13318) covalent geometry : angle 0.59104 (18065) SS BOND : bond 0.00177 ( 3) SS BOND : angle 1.69186 ( 6) hydrogen bonds : bond 0.04409 ( 744) hydrogen bonds : angle 4.57512 ( 2205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 TRP cc_start: 0.6130 (m100) cc_final: 0.5473 (m100) REVERT: A 402 MET cc_start: 0.5931 (tmm) cc_final: 0.3142 (mmt) REVERT: A 590 PHE cc_start: 0.7003 (m-80) cc_final: 0.6633 (m-80) REVERT: A 626 PHE cc_start: 0.6725 (OUTLIER) cc_final: 0.5951 (t80) REVERT: A 640 MET cc_start: 0.5884 (pmm) cc_final: 0.5554 (pmm) REVERT: A 678 ILE cc_start: 0.8056 (mt) cc_final: 0.7834 (mt) REVERT: A 721 ILE cc_start: 0.8225 (mm) cc_final: 0.7967 (tp) REVERT: A 732 TRP cc_start: 0.6493 (p-90) cc_final: 0.6141 (p-90) REVERT: B 748 TYR cc_start: 0.7158 (t80) cc_final: 0.6822 (t80) REVERT: B 776 ARG cc_start: 0.7616 (tpp80) cc_final: 0.7360 (ttm170) REVERT: B 1072 MET cc_start: 0.8082 (tpt) cc_final: 0.7871 (mmm) outliers start: 22 outliers final: 16 residues processed: 225 average time/residue: 0.0937 time to fit residues: 33.3408 Evaluate side-chains 212 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 126 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN B 830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.216915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163045 restraints weight = 16800.130| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.28 r_work: 0.3760 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13321 Z= 0.176 Angle : 0.600 9.201 18071 Z= 0.313 Chirality : 0.044 0.245 2082 Planarity : 0.005 0.058 2243 Dihedral : 6.373 85.196 1780 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.22 % Allowed : 12.97 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1655 helix: 0.91 (0.16), residues: 974 sheet: -1.07 (0.45), residues: 127 loop : -2.17 (0.23), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1064 TYR 0.017 0.001 TYR A 353 PHE 0.032 0.002 PHE B 728 TRP 0.024 0.001 TRP A 300 HIS 0.005 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00408 (13318) covalent geometry : angle 0.59775 (18065) SS BOND : bond 0.00127 ( 3) SS BOND : angle 2.62272 ( 6) hydrogen bonds : bond 0.04282 ( 744) hydrogen bonds : angle 4.51908 ( 2205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 300 TRP cc_start: 0.6086 (m100) cc_final: 0.5706 (m100) REVERT: A 402 MET cc_start: 0.5925 (tmm) cc_final: 0.3146 (mmt) REVERT: A 590 PHE cc_start: 0.7165 (m-80) cc_final: 0.6783 (m-80) REVERT: A 626 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6005 (t80) REVERT: A 640 MET cc_start: 0.5864 (pmm) cc_final: 0.5593 (pmm) REVERT: A 678 ILE cc_start: 0.8089 (mt) cc_final: 0.7857 (mt) REVERT: A 721 ILE cc_start: 0.8202 (mm) cc_final: 0.7904 (tp) REVERT: A 732 TRP cc_start: 0.6523 (p-90) cc_final: 0.6160 (p-90) REVERT: A 1151 ARG cc_start: 0.8816 (tpt170) cc_final: 0.8505 (tpt170) REVERT: B 748 TYR cc_start: 0.7166 (t80) cc_final: 0.6788 (t80) outliers start: 31 outliers final: 20 residues processed: 230 average time/residue: 0.0933 time to fit residues: 33.4950 Evaluate side-chains 220 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 0 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 111 optimal weight: 0.0970 chunk 7 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 830 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.217968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.168190 restraints weight = 16830.644| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.14 r_work: 0.3820 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13321 Z= 0.149 Angle : 0.598 12.970 18071 Z= 0.309 Chirality : 0.043 0.194 2082 Planarity : 0.005 0.072 2243 Dihedral : 6.302 84.846 1780 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.58 % Allowed : 14.48 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1655 helix: 0.93 (0.16), residues: 974 sheet: -1.10 (0.45), residues: 127 loop : -2.17 (0.23), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1064 TYR 0.017 0.001 TYR A 353 PHE 0.032 0.002 PHE B 728 TRP 0.020 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00343 (13318) covalent geometry : angle 0.59713 (18065) SS BOND : bond 0.00198 ( 3) SS BOND : angle 2.21930 ( 6) hydrogen bonds : bond 0.04136 ( 744) hydrogen bonds : angle 4.49677 ( 2205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 300 TRP cc_start: 0.5704 (m100) cc_final: 0.5414 (m100) REVERT: A 402 MET cc_start: 0.5943 (tmm) cc_final: 0.3163 (mmt) REVERT: A 590 PHE cc_start: 0.7113 (m-80) cc_final: 0.6826 (m-80) REVERT: A 626 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5964 (t80) REVERT: A 640 MET cc_start: 0.5884 (pmm) cc_final: 0.5613 (pmm) REVERT: A 721 ILE cc_start: 0.8180 (mm) cc_final: 0.7886 (tp) REVERT: A 732 TRP cc_start: 0.6505 (p-90) cc_final: 0.6158 (p-90) REVERT: B 297 LEU cc_start: 0.8608 (mt) cc_final: 0.7814 (pp) REVERT: B 748 TYR cc_start: 0.7192 (t80) cc_final: 0.6824 (t80) REVERT: B 1072 MET cc_start: 0.7919 (tpt) cc_final: 0.7686 (mmm) outliers start: 36 outliers final: 24 residues processed: 224 average time/residue: 0.0932 time to fit residues: 32.6449 Evaluate side-chains 214 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.0870 chunk 104 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 148 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.212981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.158936 restraints weight = 16672.716| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.46 r_work: 0.3717 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13321 Z= 0.134 Angle : 0.594 14.061 18071 Z= 0.304 Chirality : 0.042 0.163 2082 Planarity : 0.005 0.079 2243 Dihedral : 6.175 84.092 1780 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.22 % Allowed : 15.84 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.20), residues: 1655 helix: 1.03 (0.16), residues: 975 sheet: -0.89 (0.47), residues: 123 loop : -2.16 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1064 TYR 0.016 0.001 TYR B 584 PHE 0.033 0.002 PHE B 728 TRP 0.015 0.001 TRP A 300 HIS 0.008 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00300 (13318) covalent geometry : angle 0.59249 (18065) SS BOND : bond 0.00196 ( 3) SS BOND : angle 2.01680 ( 6) hydrogen bonds : bond 0.03983 ( 744) hydrogen bonds : angle 4.42531 ( 2205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 TRP cc_start: 0.5710 (m-10) cc_final: 0.5417 (m100) REVERT: A 390 THR cc_start: 0.7900 (m) cc_final: 0.7696 (p) REVERT: A 402 MET cc_start: 0.5826 (tmm) cc_final: 0.3023 (mmt) REVERT: A 590 PHE cc_start: 0.7068 (m-80) cc_final: 0.6806 (m-80) REVERT: A 626 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6072 (t80) REVERT: A 640 MET cc_start: 0.5841 (pmm) cc_final: 0.5587 (pmm) REVERT: A 677 ILE cc_start: 0.7158 (mt) cc_final: 0.6829 (tp) REVERT: A 678 ILE cc_start: 0.8247 (mt) cc_final: 0.7805 (mt) REVERT: A 679 SER cc_start: 0.8155 (t) cc_final: 0.7593 (p) REVERT: A 681 PHE cc_start: 0.8064 (m-80) cc_final: 0.7348 (m-80) REVERT: A 721 ILE cc_start: 0.8078 (mm) cc_final: 0.7767 (tp) REVERT: A 732 TRP cc_start: 0.6444 (p-90) cc_final: 0.6088 (p-90) REVERT: A 839 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: B 297 LEU cc_start: 0.8590 (mt) cc_final: 0.7781 (pp) REVERT: B 748 TYR cc_start: 0.7050 (t80) cc_final: 0.6735 (t80) REVERT: B 794 MET cc_start: 0.8855 (mmm) cc_final: 0.8496 (mmm) outliers start: 31 outliers final: 24 residues processed: 218 average time/residue: 0.0935 time to fit residues: 32.1945 Evaluate side-chains 223 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.201329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.143034 restraints weight = 16966.721| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.66 r_work: 0.3523 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13321 Z= 0.268 Angle : 0.707 14.746 18071 Z= 0.363 Chirality : 0.047 0.188 2082 Planarity : 0.005 0.075 2243 Dihedral : 6.378 85.335 1780 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.80 % Allowed : 16.99 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.20), residues: 1655 helix: 0.77 (0.16), residues: 976 sheet: -1.24 (0.45), residues: 126 loop : -2.28 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 546 TYR 0.023 0.002 TYR A 739 PHE 0.031 0.003 PHE B 728 TRP 0.025 0.002 TRP A 300 HIS 0.007 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00645 (13318) covalent geometry : angle 0.70581 (18065) SS BOND : bond 0.00113 ( 3) SS BOND : angle 1.93511 ( 6) hydrogen bonds : bond 0.04515 ( 744) hydrogen bonds : angle 4.68265 ( 2205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 ARG cc_start: 0.6187 (ptm160) cc_final: 0.5864 (mtp-110) REVERT: A 590 PHE cc_start: 0.7176 (m-80) cc_final: 0.6926 (m-80) REVERT: A 626 PHE cc_start: 0.6639 (OUTLIER) cc_final: 0.5973 (t80) REVERT: A 640 MET cc_start: 0.5829 (pmm) cc_final: 0.5574 (pmm) REVERT: A 679 SER cc_start: 0.8289 (t) cc_final: 0.7730 (p) REVERT: A 681 PHE cc_start: 0.8087 (m-80) cc_final: 0.7480 (m-80) REVERT: A 732 TRP cc_start: 0.6512 (p-90) cc_final: 0.6189 (p-90) REVERT: A 839 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8259 (tp40) REVERT: B 297 LEU cc_start: 0.8662 (mt) cc_final: 0.7900 (pp) REVERT: B 748 TYR cc_start: 0.7096 (t80) cc_final: 0.6723 (t80) outliers start: 39 outliers final: 29 residues processed: 224 average time/residue: 0.0959 time to fit residues: 33.6533 Evaluate side-chains 224 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 103 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.203309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148146 restraints weight = 16733.663| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.45 r_work: 0.3574 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13321 Z= 0.173 Angle : 0.647 14.143 18071 Z= 0.330 Chirality : 0.044 0.193 2082 Planarity : 0.005 0.071 2243 Dihedral : 6.293 82.948 1780 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.65 % Allowed : 17.56 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1655 helix: 0.81 (0.16), residues: 978 sheet: -1.31 (0.44), residues: 127 loop : -2.32 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1064 TYR 0.030 0.001 TYR A 739 PHE 0.039 0.002 PHE B 728 TRP 0.013 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00411 (13318) covalent geometry : angle 0.64468 (18065) SS BOND : bond 0.00143 ( 3) SS BOND : angle 2.93854 ( 6) hydrogen bonds : bond 0.04173 ( 744) hydrogen bonds : angle 4.56509 ( 2205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 ARG cc_start: 0.6193 (ptm160) cc_final: 0.5864 (mtp-110) REVERT: A 303 MET cc_start: 0.4883 (ttm) cc_final: 0.4480 (ttp) REVERT: A 402 MET cc_start: 0.5965 (tmm) cc_final: 0.3175 (mmt) REVERT: A 590 PHE cc_start: 0.7247 (m-80) cc_final: 0.7016 (m-80) REVERT: A 626 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.5944 (t80) REVERT: A 640 MET cc_start: 0.5947 (pmm) cc_final: 0.5599 (pmm) REVERT: A 679 SER cc_start: 0.8213 (t) cc_final: 0.7618 (p) REVERT: A 721 ILE cc_start: 0.8117 (mm) cc_final: 0.7846 (tp) REVERT: A 732 TRP cc_start: 0.6516 (p-90) cc_final: 0.6184 (p-90) REVERT: A 829 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6458 (mmt180) REVERT: A 839 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8248 (tp40) REVERT: B 297 LEU cc_start: 0.8607 (mt) cc_final: 0.7817 (pp) REVERT: B 748 TYR cc_start: 0.7090 (t80) cc_final: 0.6728 (t80) REVERT: B 862 ASP cc_start: 0.7936 (p0) cc_final: 0.7670 (p0) REVERT: B 865 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7688 (mt-10) outliers start: 37 outliers final: 27 residues processed: 215 average time/residue: 0.0948 time to fit residues: 31.7587 Evaluate side-chains 219 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 724 CYS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1209 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 165 optimal weight: 0.4980 chunk 116 optimal weight: 0.9980 chunk 151 optimal weight: 0.0020 chunk 146 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 786 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.205285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.149386 restraints weight = 16872.350| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.78 r_work: 0.3613 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13321 Z= 0.139 Angle : 0.619 14.016 18071 Z= 0.316 Chirality : 0.043 0.217 2082 Planarity : 0.005 0.063 2243 Dihedral : 6.116 80.711 1780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.22 % Allowed : 18.06 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1655 helix: 0.93 (0.16), residues: 978 sheet: -1.22 (0.45), residues: 125 loop : -2.34 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1064 TYR 0.027 0.001 TYR A 739 PHE 0.033 0.002 PHE B 728 TRP 0.010 0.001 TRP A 300 HIS 0.008 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00323 (13318) covalent geometry : angle 0.61737 (18065) SS BOND : bond 0.00216 ( 3) SS BOND : angle 2.66621 ( 6) hydrogen bonds : bond 0.03980 ( 744) hydrogen bonds : angle 4.48061 ( 2205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 294 ARG cc_start: 0.6057 (ptm160) cc_final: 0.5547 (mtp-110) REVERT: A 626 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6093 (t80) REVERT: A 640 MET cc_start: 0.5948 (pmm) cc_final: 0.5584 (pmm) REVERT: A 679 SER cc_start: 0.8122 (t) cc_final: 0.7633 (p) REVERT: A 713 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6173 (ptm) REVERT: A 721 ILE cc_start: 0.8052 (mm) cc_final: 0.7769 (tp) REVERT: A 732 TRP cc_start: 0.6437 (p-90) cc_final: 0.6113 (p-90) REVERT: A 829 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6391 (mmt180) REVERT: A 839 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8196 (tp40) REVERT: B 297 LEU cc_start: 0.8595 (mt) cc_final: 0.7805 (pp) REVERT: B 576 SER cc_start: 0.7257 (t) cc_final: 0.7047 (p) REVERT: B 748 TYR cc_start: 0.6965 (t80) cc_final: 0.6655 (t80) outliers start: 31 outliers final: 21 residues processed: 218 average time/residue: 0.0906 time to fit residues: 30.8181 Evaluate side-chains 218 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 724 CYS Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 786 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.202711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145588 restraints weight = 16975.074| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.59 r_work: 0.3557 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13321 Z= 0.206 Angle : 0.681 13.430 18071 Z= 0.348 Chirality : 0.045 0.214 2082 Planarity : 0.005 0.060 2243 Dihedral : 6.215 81.481 1780 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.72 % Allowed : 18.21 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1655 helix: 0.78 (0.16), residues: 980 sheet: -1.30 (0.45), residues: 123 loop : -2.35 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 898 TYR 0.030 0.002 TYR A 739 PHE 0.054 0.002 PHE B 659 TRP 0.015 0.001 TRP A 300 HIS 0.007 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00491 (13318) covalent geometry : angle 0.68001 (18065) SS BOND : bond 0.00197 ( 3) SS BOND : angle 2.49689 ( 6) hydrogen bonds : bond 0.04245 ( 744) hydrogen bonds : angle 4.60961 ( 2205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 294 ARG cc_start: 0.6060 (ptm160) cc_final: 0.5557 (mtp-110) REVERT: A 300 TRP cc_start: 0.6202 (m-10) cc_final: 0.5558 (m100) REVERT: A 402 MET cc_start: 0.5669 (tmm) cc_final: 0.3175 (mmt) REVERT: A 626 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 640 MET cc_start: 0.5930 (pmm) cc_final: 0.5593 (pmm) REVERT: A 679 SER cc_start: 0.8113 (t) cc_final: 0.7708 (p) REVERT: A 681 PHE cc_start: 0.7840 (m-80) cc_final: 0.7471 (m-80) REVERT: A 721 ILE cc_start: 0.8039 (mm) cc_final: 0.7812 (tp) REVERT: A 732 TRP cc_start: 0.6451 (p-90) cc_final: 0.6131 (p-90) REVERT: A 839 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8206 (tp40) REVERT: A 1151 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8578 (tpt170) REVERT: B 297 LEU cc_start: 0.8658 (mt) cc_final: 0.7882 (pp) REVERT: B 339 SER cc_start: 0.6435 (m) cc_final: 0.6000 (p) REVERT: B 576 SER cc_start: 0.7265 (t) cc_final: 0.7060 (p) REVERT: B 748 TYR cc_start: 0.6964 (t80) cc_final: 0.6644 (t80) REVERT: B 1072 MET cc_start: 0.8101 (tpt) cc_final: 0.7872 (mmm) outliers start: 24 outliers final: 21 residues processed: 205 average time/residue: 0.0993 time to fit residues: 31.4345 Evaluate side-chains 214 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 839 GLN Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1092 ILE Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 721 ILE Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1087 MET Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 67 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 22 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.205143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.147405 restraints weight = 16775.885| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.75 r_work: 0.3584 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13321 Z= 0.146 Angle : 0.644 12.963 18071 Z= 0.327 Chirality : 0.043 0.247 2082 Planarity : 0.005 0.062 2243 Dihedral : 6.095 79.612 1780 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.86 % Allowed : 17.99 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.20), residues: 1655 helix: 0.83 (0.16), residues: 980 sheet: -1.51 (0.43), residues: 134 loop : -2.34 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1064 TYR 0.035 0.001 TYR A 739 PHE 0.041 0.002 PHE B 728 TRP 0.013 0.001 TRP A 892 HIS 0.007 0.001 HIS A1067 Details of bonding type rmsd covalent geometry : bond 0.00337 (13318) covalent geometry : angle 0.64276 (18065) SS BOND : bond 0.00231 ( 3) SS BOND : angle 2.52667 ( 6) hydrogen bonds : bond 0.04000 ( 744) hydrogen bonds : angle 4.52947 ( 2205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3531.81 seconds wall clock time: 61 minutes 13.67 seconds (3673.67 seconds total)