Starting phenix.real_space_refine on Fri Mar 15 03:21:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/03_2024/5xwy_6777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/03_2024/5xwy_6777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/03_2024/5xwy_6777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/03_2024/5xwy_6777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/03_2024/5xwy_6777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xwy_6777/03_2024/5xwy_6777.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 P 51 5.49 5 S 24 5.16 5 C 6528 2.51 5 N 1784 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A ARG 909": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9407 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 13, 'PTRANS': 10, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1086 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 12} Link IDs: {'rna2p': 17, 'rna3p': 33} Chain breaks: 1 Time building chain proxies: 5.83, per 1000 atoms: 0.56 Number of scatterers: 10493 At special positions: 0 Unit cell: (113.16, 111.52, 107.42, 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) S 24 16.00 P 51 15.00 O 2106 8.00 N 1784 7.00 C 6528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.07 Conformation dependent library (CDL) restraints added in 1.6 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 5 sheets defined 63.7% alpha, 2.9% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 59 through 69 removed outlier: 4.058A pdb=" N LYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.524A pdb=" N TYR A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 removed outlier: 3.911A pdb=" N VAL A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.945A pdb=" N LYS A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.746A pdb=" N ILE A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.707A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.993A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.838A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.551A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.590A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.522A pdb=" N TYR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.767A pdb=" N LYS A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.907A pdb=" N LYS A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 354 removed outlier: 3.663A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 393 removed outlier: 3.651A pdb=" N PHE A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.761A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.515A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.511A pdb=" N ALA A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.555A pdb=" N LYS A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.904A pdb=" N TYR A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.679A pdb=" N GLU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.670A pdb=" N ILE A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 4.128A pdb=" N LYS A 642 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.549A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.571A pdb=" N ILE A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 removed outlier: 3.957A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.639A pdb=" N GLN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.225A pdb=" N PHE A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 767 removed outlier: 3.835A pdb=" N ASN A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'A' and resid 796 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 834 through 842 removed outlier: 3.551A pdb=" N LYS A 839 " --> pdb=" O ASN A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 removed outlier: 4.419A pdb=" N ASN A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 883 through 895 removed outlier: 3.532A pdb=" N TYR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.530A pdb=" N LYS A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 946 removed outlier: 3.608A pdb=" N SER A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 944 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 removed outlier: 3.907A pdb=" N GLY A 966 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 990 Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 4.233A pdb=" N LYS A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 4.246A pdb=" N VAL A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 3.556A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.527A pdb=" N GLU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 3.815A pdb=" N LYS A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.750A pdb=" N LYS A1145 " --> pdb=" O CYS A1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.668A pdb=" N LYS A 165 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 160 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA5, first strand: chain 'A' and resid 1099 through 1104 removed outlier: 3.554A pdb=" N THR A1114 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS A1103 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A1112 " --> pdb=" O LYS A1103 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2337 1.33 - 1.45: 2437 1.45 - 1.57: 5856 1.57 - 1.68: 102 1.68 - 1.80: 45 Bond restraints: 10777 Sorted by residual: bond pdb=" CA ILE A 402 " pdb=" CB ILE A 402 " ideal model delta sigma weight residual 1.540 1.586 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.77e+00 bond pdb=" CA THR A 403 " pdb=" C THR A 403 " ideal model delta sigma weight residual 1.525 1.554 -0.029 1.11e-02 8.12e+03 6.68e+00 bond pdb=" N ASN A 696 " pdb=" CA ASN A 696 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.40e+00 ... (remaining 10772 not shown) Histogram of bond angle deviations from ideal: 98.82 - 106.78: 438 106.78 - 114.75: 6302 114.75 - 122.72: 6983 122.72 - 130.69: 892 130.69 - 138.66: 55 Bond angle restraints: 14670 Sorted by residual: angle pdb=" C GLU A 544 " pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 121.70 138.66 -16.96 1.80e+00 3.09e-01 8.88e+01 angle pdb=" C MET A 44 " pdb=" N TYR A 45 " pdb=" CA TYR A 45 " ideal model delta sigma weight residual 121.70 135.33 -13.63 1.80e+00 3.09e-01 5.73e+01 angle pdb=" C ASP A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 121.97 135.52 -13.55 1.80e+00 3.09e-01 5.67e+01 angle pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLY A 404 " ideal model delta sigma weight residual 116.35 126.09 -9.74 1.30e+00 5.92e-01 5.61e+01 angle pdb=" C GLY A 866 " pdb=" N MET A 867 " pdb=" CA MET A 867 " ideal model delta sigma weight residual 121.70 133.48 -11.78 1.80e+00 3.09e-01 4.28e+01 ... (remaining 14665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 6478 35.24 - 70.47: 158 70.47 - 105.71: 19 105.71 - 140.94: 3 140.94 - 176.18: 1 Dihedral angle restraints: 6659 sinusoidal: 3319 harmonic: 3340 Sorted by residual: dihedral pdb=" CA ASP A 401 " pdb=" C ASP A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -54.57 -125.43 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta harmonic sigma weight residual 180.00 67.50 112.50 0 5.00e+00 4.00e-02 5.06e+02 dihedral pdb=" CA LEU A 312 " pdb=" C LEU A 312 " pdb=" N SER A 313 " pdb=" CA SER A 313 " ideal model delta harmonic sigma weight residual 0.00 -40.28 40.28 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 6656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1545 0.124 - 0.247: 62 0.247 - 0.371: 7 0.371 - 0.494: 0 0.494 - 0.618: 1 Chirality restraints: 1615 Sorted by residual: chirality pdb=" CB ILE A 704 " pdb=" CA ILE A 704 " pdb=" CG1 ILE A 704 " pdb=" CG2 ILE A 704 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLU A 671 " pdb=" N GLU A 671 " pdb=" C GLU A 671 " pdb=" CB GLU A 671 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1612 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 677 " -0.018 2.00e-02 2.50e+03 1.77e-02 6.30e+00 pdb=" CG TYR A 677 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 677 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 677 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 677 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 677 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 677 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 677 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 202 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C GLU A 202 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 202 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 203 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 608 " -0.023 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE A 608 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 608 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 608 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 608 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 608 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 608 " -0.002 2.00e-02 2.50e+03 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2743 2.79 - 3.32: 9358 3.32 - 3.85: 17183 3.85 - 4.37: 21345 4.37 - 4.90: 34501 Nonbonded interactions: 85130 Sorted by model distance: nonbonded pdb=" O ILE A1120 " pdb=" OG1 THR A1133 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR A 178 " pdb=" OD1 ASP A 285 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR A 662 " pdb=" O2' A B 30 " model vdw 2.291 2.440 nonbonded pdb=" OD1 ASN A 378 " pdb=" OG SER A 780 " model vdw 2.306 2.440 nonbonded pdb=" NZ LYS A 5 " pdb=" OP2 G B 23 " model vdw 2.307 2.520 ... (remaining 85125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.340 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: 2.230 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.330 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.008 0.080 10777 Z= 0.489 Angle : 1.175 20.001 14670 Z= 0.623 Chirality : 0.061 0.618 1615 Planarity : 0.005 0.037 1682 Dihedral : 14.685 176.181 4503 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.87 % Allowed : 6.46 % Favored : 92.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.91 % Twisted Proline : 0.00 % Twisted General : 0.82 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.96 (0.15), residues: 1109 helix: -4.22 (0.08), residues: 692 sheet: -2.31 (0.91), residues: 30 loop : -3.12 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 971 HIS 0.016 0.003 HIS A 228 PHE 0.042 0.004 PHE A 608 TYR 0.043 0.003 TYR A 677 ARG 0.013 0.001 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 289 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8060 (m-30) cc_final: 0.7649 (p0) REVERT: A 202 GLU cc_start: 0.7796 (tp30) cc_final: 0.7459 (tt0) REVERT: A 207 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8220 (mttp) REVERT: A 247 GLU cc_start: 0.5238 (mm-30) cc_final: 0.4412 (mm-30) REVERT: A 393 ILE cc_start: 0.9108 (tt) cc_final: 0.8891 (tt) REVERT: A 424 GLU cc_start: 0.6787 (mp0) cc_final: 0.6501 (mm-30) REVERT: A 501 LYS cc_start: 0.8429 (tttm) cc_final: 0.8167 (tppt) REVERT: A 542 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7967 (ttm-80) REVERT: A 618 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 629 ASP cc_start: 0.4729 (t70) cc_final: 0.4516 (t0) REVERT: A 631 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6084 (pmt100) REVERT: A 758 ARG cc_start: 0.8247 (ptt-90) cc_final: 0.7925 (ptp-170) REVERT: A 832 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7994 (p) REVERT: A 888 LYS cc_start: 0.8631 (ttpm) cc_final: 0.8414 (ttpp) REVERT: A 974 ASP cc_start: 0.8294 (m-30) cc_final: 0.8087 (m-30) REVERT: A 1008 ILE cc_start: 0.8741 (mt) cc_final: 0.8390 (mp) REVERT: A 1094 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8344 (ttmm) REVERT: A 1118 GLU cc_start: 0.7869 (pp20) cc_final: 0.7646 (tp30) REVERT: A 1142 LYS cc_start: 0.8362 (mttt) cc_final: 0.8016 (mttp) outliers start: 9 outliers final: 2 residues processed: 295 average time/residue: 0.3147 time to fit residues: 119.6606 Evaluate side-chains 202 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 84 ASN A 151 ASN A 173 ASN A 191 ASN A 294 HIS A 369 ASN A 400 ASN A 492 ASN A 547 ASN A 611 ASN A 626 ASN A 665 ASN A 771 HIS A 776 ASN A 785 GLN A 808 ASN A 908 HIS A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10777 Z= 0.178 Angle : 0.703 12.175 14670 Z= 0.375 Chirality : 0.041 0.281 1615 Planarity : 0.004 0.037 1682 Dihedral : 16.254 175.177 1980 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 3.09 % Allowed : 9.84 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.21), residues: 1109 helix: -2.07 (0.15), residues: 720 sheet: -1.67 (1.04), residues: 25 loop : -2.76 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 971 HIS 0.008 0.001 HIS A 228 PHE 0.033 0.002 PHE A 478 TYR 0.017 0.002 TYR A 677 ARG 0.005 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.7709 (tppt) cc_final: 0.7229 (mmmt) REVERT: A 31 ASP cc_start: 0.8134 (m-30) cc_final: 0.7756 (p0) REVERT: A 150 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8206 (mmmm) REVERT: A 178 TYR cc_start: 0.8654 (t80) cc_final: 0.7950 (t80) REVERT: A 202 GLU cc_start: 0.7855 (tp30) cc_final: 0.7489 (tt0) REVERT: A 207 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8234 (mttp) REVERT: A 208 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8362 (tp) REVERT: A 254 MET cc_start: 0.7778 (tpt) cc_final: 0.6420 (tpt) REVERT: A 424 GLU cc_start: 0.6749 (mp0) cc_final: 0.6484 (mm-30) REVERT: A 501 LYS cc_start: 0.8285 (tttm) cc_final: 0.8002 (tppt) REVERT: A 510 LYS cc_start: 0.8645 (tmtm) cc_final: 0.8412 (tppt) REVERT: A 542 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7882 (ttm-80) REVERT: A 631 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5620 (ptt90) REVERT: A 773 GLU cc_start: 0.7570 (tp30) cc_final: 0.7325 (tp30) REVERT: A 831 LYS cc_start: 0.7958 (mttm) cc_final: 0.7690 (mttp) REVERT: A 893 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7782 (mtpp) REVERT: A 1008 ILE cc_start: 0.8793 (mt) cc_final: 0.8415 (mp) REVERT: A 1017 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7987 (mtmt) REVERT: A 1094 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8179 (ttmm) REVERT: A 1118 GLU cc_start: 0.8014 (pp20) cc_final: 0.7726 (tp30) REVERT: A 1142 LYS cc_start: 0.8302 (mttt) cc_final: 0.8000 (mttp) outliers start: 32 outliers final: 9 residues processed: 232 average time/residue: 0.2958 time to fit residues: 90.1278 Evaluate side-chains 176 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN A 378 ASN A 731 ASN A 828 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1049 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10777 Z= 0.318 Angle : 0.735 12.911 14670 Z= 0.384 Chirality : 0.045 0.372 1615 Planarity : 0.004 0.033 1682 Dihedral : 16.150 173.883 1975 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.12 % Favored : 92.70 % Rotamer: Outliers : 4.15 % Allowed : 11.19 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.23), residues: 1109 helix: -0.94 (0.18), residues: 722 sheet: -1.35 (0.95), residues: 30 loop : -2.52 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 971 HIS 0.008 0.001 HIS A 228 PHE 0.024 0.003 PHE A 478 TYR 0.030 0.002 TYR A 677 ARG 0.005 0.001 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8376 (m-30) cc_final: 0.7960 (p0) REVERT: A 150 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8262 (mmmm) REVERT: A 154 ASN cc_start: 0.7974 (m-40) cc_final: 0.7515 (t0) REVERT: A 178 TYR cc_start: 0.8698 (t80) cc_final: 0.8276 (t80) REVERT: A 207 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8268 (mttp) REVERT: A 208 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8376 (tp) REVERT: A 254 MET cc_start: 0.8113 (tpt) cc_final: 0.6991 (tpt) REVERT: A 424 GLU cc_start: 0.6953 (mp0) cc_final: 0.6680 (mm-30) REVERT: A 501 LYS cc_start: 0.8301 (tttm) cc_final: 0.7972 (mmtp) REVERT: A 510 LYS cc_start: 0.8720 (tmtm) cc_final: 0.8506 (tppt) REVERT: A 542 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8098 (ttm-80) REVERT: A 587 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7225 (mt-10) REVERT: A 618 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7348 (mm) REVERT: A 773 GLU cc_start: 0.7651 (tp30) cc_final: 0.7327 (tp30) REVERT: A 952 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 1008 ILE cc_start: 0.8863 (mt) cc_final: 0.8499 (mp) REVERT: A 1068 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (mm) REVERT: A 1094 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8268 (ttmm) REVERT: A 1118 GLU cc_start: 0.8228 (pp20) cc_final: 0.7966 (tp30) REVERT: A 1142 LYS cc_start: 0.8449 (mttt) cc_final: 0.8138 (mttp) outliers start: 43 outliers final: 19 residues processed: 216 average time/residue: 0.2868 time to fit residues: 81.6975 Evaluate side-chains 194 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 378 ASN A 432 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10777 Z= 0.258 Angle : 0.671 12.608 14670 Z= 0.354 Chirality : 0.043 0.406 1615 Planarity : 0.003 0.027 1682 Dihedral : 15.968 172.698 1975 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 2.99 % Allowed : 13.79 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.25), residues: 1109 helix: -0.31 (0.19), residues: 723 sheet: -1.24 (0.95), residues: 30 loop : -2.44 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 PHE 0.022 0.002 PHE A 848 TYR 0.021 0.001 TYR A 677 ARG 0.004 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7874 (pp20) cc_final: 0.7156 (pp20) REVERT: A 31 ASP cc_start: 0.8357 (m-30) cc_final: 0.7989 (p0) REVERT: A 150 LYS cc_start: 0.8777 (mmmt) cc_final: 0.8226 (mmmm) REVERT: A 178 TYR cc_start: 0.8702 (t80) cc_final: 0.8276 (t80) REVERT: A 202 GLU cc_start: 0.7833 (tp30) cc_final: 0.7311 (tt0) REVERT: A 208 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8342 (tp) REVERT: A 254 MET cc_start: 0.8295 (tpt) cc_final: 0.7137 (tpt) REVERT: A 424 GLU cc_start: 0.7016 (mp0) cc_final: 0.6655 (mm-30) REVERT: A 501 LYS cc_start: 0.8255 (tttm) cc_final: 0.7940 (mmtp) REVERT: A 510 LYS cc_start: 0.8721 (tmtm) cc_final: 0.8511 (tppt) REVERT: A 542 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7631 (ttt90) REVERT: A 773 GLU cc_start: 0.7653 (tp30) cc_final: 0.7320 (tp30) REVERT: A 933 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 952 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 1008 ILE cc_start: 0.8807 (mt) cc_final: 0.8500 (mp) REVERT: A 1094 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8245 (ttmm) REVERT: A 1118 GLU cc_start: 0.8232 (pp20) cc_final: 0.7973 (tp30) REVERT: A 1142 LYS cc_start: 0.8446 (mttt) cc_final: 0.8146 (mttp) outliers start: 31 outliers final: 17 residues processed: 205 average time/residue: 0.2938 time to fit residues: 80.2856 Evaluate side-chains 188 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN A 719 GLN A 771 HIS A 930 GLN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10777 Z= 0.295 Angle : 0.684 12.493 14670 Z= 0.361 Chirality : 0.044 0.372 1615 Planarity : 0.003 0.036 1682 Dihedral : 15.937 172.098 1973 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer: Outliers : 3.86 % Allowed : 14.46 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.25), residues: 1109 helix: -0.08 (0.19), residues: 723 sheet: -1.04 (1.01), residues: 30 loop : -2.35 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 PHE 0.025 0.002 PHE A 848 TYR 0.021 0.002 TYR A 677 ARG 0.004 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7886 (pp20) cc_final: 0.7144 (pp20) REVERT: A 31 ASP cc_start: 0.8364 (m-30) cc_final: 0.8055 (p0) REVERT: A 150 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8233 (mmmm) REVERT: A 178 TYR cc_start: 0.8746 (t80) cc_final: 0.8336 (t80) REVERT: A 208 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 254 MET cc_start: 0.8331 (tpt) cc_final: 0.7214 (tpt) REVERT: A 334 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 378 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8125 (t0) REVERT: A 424 GLU cc_start: 0.7135 (mp0) cc_final: 0.6863 (mm-30) REVERT: A 439 GLU cc_start: 0.8336 (tp30) cc_final: 0.8104 (tp30) REVERT: A 501 LYS cc_start: 0.8283 (tttm) cc_final: 0.7969 (mmtp) REVERT: A 510 LYS cc_start: 0.8753 (tmtm) cc_final: 0.8552 (tppt) REVERT: A 542 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.7613 (ttt90) REVERT: A 587 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 773 GLU cc_start: 0.7655 (tp30) cc_final: 0.7247 (tp30) REVERT: A 952 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8260 (tt) REVERT: A 1008 ILE cc_start: 0.8833 (mt) cc_final: 0.8500 (mp) REVERT: A 1094 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8291 (ttmm) REVERT: A 1118 GLU cc_start: 0.8269 (pp20) cc_final: 0.7974 (tp30) REVERT: A 1142 LYS cc_start: 0.8476 (mttt) cc_final: 0.8155 (mttp) outliers start: 40 outliers final: 25 residues processed: 205 average time/residue: 0.2920 time to fit residues: 79.4856 Evaluate side-chains 199 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10777 Z= 0.212 Angle : 0.637 12.099 14670 Z= 0.340 Chirality : 0.042 0.380 1615 Planarity : 0.003 0.031 1682 Dihedral : 15.811 171.430 1973 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 3.28 % Allowed : 15.43 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1109 helix: 0.20 (0.20), residues: 725 sheet: -0.99 (1.03), residues: 30 loop : -2.41 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.005 0.001 HIS A 228 PHE 0.019 0.002 PHE A 848 TYR 0.016 0.001 TYR A 677 ARG 0.004 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 171 time to evaluate : 1.095 Fit side-chains REVERT: A 26 GLU cc_start: 0.7859 (pp20) cc_final: 0.7169 (pp20) REVERT: A 31 ASP cc_start: 0.8352 (m-30) cc_final: 0.8016 (p0) REVERT: A 150 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8180 (mmmm) REVERT: A 178 TYR cc_start: 0.8746 (t80) cc_final: 0.8278 (t80) REVERT: A 208 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8352 (tp) REVERT: A 254 MET cc_start: 0.8373 (tpt) cc_final: 0.7207 (tpt) REVERT: A 334 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 424 GLU cc_start: 0.6876 (mp0) cc_final: 0.6641 (mm-30) REVERT: A 439 GLU cc_start: 0.8339 (tp30) cc_final: 0.7974 (tp30) REVERT: A 501 LYS cc_start: 0.8250 (tttm) cc_final: 0.7956 (mmtp) REVERT: A 502 MET cc_start: 0.8158 (ttm) cc_final: 0.7856 (ttp) REVERT: A 506 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7217 (mp0) REVERT: A 542 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.7572 (ttt90) REVERT: A 773 GLU cc_start: 0.7658 (tp30) cc_final: 0.7270 (tp30) REVERT: A 952 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 978 ARG cc_start: 0.8016 (mtp180) cc_final: 0.7809 (mtm180) REVERT: A 1008 ILE cc_start: 0.8830 (mt) cc_final: 0.8483 (mp) REVERT: A 1094 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8291 (ttmm) REVERT: A 1118 GLU cc_start: 0.8251 (pp20) cc_final: 0.7990 (tp30) REVERT: A 1142 LYS cc_start: 0.8447 (mttt) cc_final: 0.8147 (mttp) outliers start: 34 outliers final: 24 residues processed: 195 average time/residue: 0.2988 time to fit residues: 76.6190 Evaluate side-chains 191 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN A 695 ASN A 930 GLN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10777 Z= 0.334 Angle : 0.699 12.200 14670 Z= 0.367 Chirality : 0.045 0.357 1615 Planarity : 0.003 0.040 1682 Dihedral : 15.786 171.885 1973 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.38 % Allowed : 16.68 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1109 helix: 0.16 (0.19), residues: 726 sheet: -0.87 (1.06), residues: 30 loop : -2.46 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 PHE 0.021 0.002 PHE A 848 TYR 0.018 0.002 TYR A 677 ARG 0.004 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.077 Fit side-chains REVERT: A 31 ASP cc_start: 0.8389 (m-30) cc_final: 0.8059 (p0) REVERT: A 150 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8228 (mmmm) REVERT: A 178 TYR cc_start: 0.8774 (t80) cc_final: 0.8394 (t80) REVERT: A 208 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8424 (tp) REVERT: A 254 MET cc_start: 0.8416 (tpt) cc_final: 0.7248 (tpt) REVERT: A 334 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: A 439 GLU cc_start: 0.8307 (tp30) cc_final: 0.7918 (tp30) REVERT: A 501 LYS cc_start: 0.8286 (tttm) cc_final: 0.7972 (mmtp) REVERT: A 502 MET cc_start: 0.8203 (ttm) cc_final: 0.7916 (ttp) REVERT: A 506 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7318 (mp0) REVERT: A 773 GLU cc_start: 0.7655 (tp30) cc_final: 0.7254 (tp30) REVERT: A 795 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (t0) REVERT: A 952 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8226 (tt) REVERT: A 1008 ILE cc_start: 0.8845 (mt) cc_final: 0.8501 (mp) REVERT: A 1094 LYS cc_start: 0.8613 (ttpt) cc_final: 0.8319 (ttmm) REVERT: A 1118 GLU cc_start: 0.8315 (pp20) cc_final: 0.7984 (tp30) REVERT: A 1142 LYS cc_start: 0.8531 (mttt) cc_final: 0.8189 (mttp) outliers start: 35 outliers final: 25 residues processed: 191 average time/residue: 0.2850 time to fit residues: 72.4121 Evaluate side-chains 192 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 695 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10777 Z= 0.168 Angle : 0.618 12.190 14670 Z= 0.330 Chirality : 0.041 0.379 1615 Planarity : 0.002 0.027 1682 Dihedral : 15.636 171.701 1973 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.18 % Allowed : 16.49 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1109 helix: 0.52 (0.20), residues: 730 sheet: -0.75 (1.05), residues: 30 loop : -2.54 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 971 HIS 0.004 0.001 HIS A 962 PHE 0.016 0.002 PHE A 814 TYR 0.012 0.001 TYR A 429 ARG 0.005 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7819 (pp20) cc_final: 0.7082 (pp20) REVERT: A 31 ASP cc_start: 0.8339 (m-30) cc_final: 0.8029 (p0) REVERT: A 150 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8095 (mmmm) REVERT: A 178 TYR cc_start: 0.8757 (t80) cc_final: 0.8241 (t80) REVERT: A 254 MET cc_start: 0.8351 (tpt) cc_final: 0.7041 (tpt) REVERT: A 312 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.4450 (pp) REVERT: A 334 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: A 439 GLU cc_start: 0.8305 (tp30) cc_final: 0.7915 (tp30) REVERT: A 501 LYS cc_start: 0.8212 (tttm) cc_final: 0.7945 (mmtp) REVERT: A 502 MET cc_start: 0.8117 (ttm) cc_final: 0.7800 (ttp) REVERT: A 506 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7240 (mp0) REVERT: A 542 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7715 (ttt90) REVERT: A 773 GLU cc_start: 0.7645 (tp30) cc_final: 0.7244 (tp30) REVERT: A 952 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 1008 ILE cc_start: 0.8793 (mt) cc_final: 0.8422 (mp) REVERT: A 1094 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8248 (ttmm) REVERT: A 1118 GLU cc_start: 0.8256 (pp20) cc_final: 0.8026 (tp30) REVERT: A 1142 LYS cc_start: 0.8464 (mttt) cc_final: 0.8173 (mttp) outliers start: 33 outliers final: 22 residues processed: 189 average time/residue: 0.3001 time to fit residues: 75.8086 Evaluate side-chains 181 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.0060 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 overall best weight: 0.9812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10777 Z= 0.174 Angle : 0.615 11.868 14670 Z= 0.327 Chirality : 0.041 0.339 1615 Planarity : 0.002 0.025 1682 Dihedral : 15.510 171.802 1973 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.51 % Allowed : 17.55 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1109 helix: 0.68 (0.20), residues: 731 sheet: -0.76 (1.02), residues: 30 loop : -2.57 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.017 0.002 PHE A 848 TYR 0.013 0.001 TYR A 677 ARG 0.005 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7748 (pp20) cc_final: 0.7095 (pp20) REVERT: A 31 ASP cc_start: 0.8323 (m-30) cc_final: 0.8012 (p0) REVERT: A 150 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8453 (mmmm) REVERT: A 178 TYR cc_start: 0.8738 (t80) cc_final: 0.8229 (t80) REVERT: A 254 MET cc_start: 0.8335 (tpt) cc_final: 0.6996 (tpt) REVERT: A 312 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.4539 (pp) REVERT: A 378 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7992 (t0) REVERT: A 501 LYS cc_start: 0.8214 (tttm) cc_final: 0.7968 (mmtp) REVERT: A 502 MET cc_start: 0.8092 (ttm) cc_final: 0.7796 (ttp) REVERT: A 506 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7273 (mp0) REVERT: A 542 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7739 (ttt90) REVERT: A 625 LEU cc_start: 0.6752 (mt) cc_final: 0.6429 (mp) REVERT: A 773 GLU cc_start: 0.7637 (tp30) cc_final: 0.7229 (tp30) REVERT: A 952 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8182 (tt) REVERT: A 978 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7267 (ttp80) REVERT: A 1008 ILE cc_start: 0.8782 (mt) cc_final: 0.8421 (mp) REVERT: A 1094 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8190 (ttmm) REVERT: A 1142 LYS cc_start: 0.8465 (mttt) cc_final: 0.8162 (mttp) outliers start: 26 outliers final: 20 residues processed: 180 average time/residue: 0.2973 time to fit residues: 70.5239 Evaluate side-chains 179 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 98 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN A 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10777 Z= 0.239 Angle : 0.651 11.963 14670 Z= 0.342 Chirality : 0.042 0.335 1615 Planarity : 0.003 0.030 1682 Dihedral : 15.492 171.944 1973 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.51 % Allowed : 18.03 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1109 helix: 0.69 (0.20), residues: 727 sheet: -0.73 (1.01), residues: 30 loop : -2.48 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.017 0.002 PHE A 848 TYR 0.017 0.001 TYR A 662 ARG 0.004 0.000 ARG A 959 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.162 Fit side-chains REVERT: A 26 GLU cc_start: 0.7841 (pp20) cc_final: 0.7102 (pp20) REVERT: A 31 ASP cc_start: 0.8327 (m-30) cc_final: 0.8017 (p0) REVERT: A 150 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8495 (mmmm) REVERT: A 178 TYR cc_start: 0.8751 (t80) cc_final: 0.8295 (t80) REVERT: A 254 MET cc_start: 0.8355 (tpt) cc_final: 0.7084 (tpt) REVERT: A 378 ASN cc_start: 0.8362 (t0) cc_final: 0.7925 (t0) REVERT: A 501 LYS cc_start: 0.8236 (tttm) cc_final: 0.7982 (mmtp) REVERT: A 502 MET cc_start: 0.8148 (ttm) cc_final: 0.7850 (ttp) REVERT: A 506 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7326 (mp0) REVERT: A 542 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7763 (ttt90) REVERT: A 773 GLU cc_start: 0.7632 (tp30) cc_final: 0.7249 (tp30) REVERT: A 795 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (t0) REVERT: A 952 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 1008 ILE cc_start: 0.8776 (mt) cc_final: 0.8448 (mp) REVERT: A 1094 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8267 (ttmm) REVERT: A 1142 LYS cc_start: 0.8492 (mttt) cc_final: 0.8183 (mttp) outliers start: 26 outliers final: 21 residues processed: 179 average time/residue: 0.3088 time to fit residues: 73.1095 Evaluate side-chains 181 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 695 ASN Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 0.0010 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN A 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.164867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129055 restraints weight = 11406.930| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.81 r_work: 0.2941 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10777 Z= 0.236 Angle : 0.653 12.004 14670 Z= 0.343 Chirality : 0.042 0.318 1615 Planarity : 0.003 0.033 1682 Dihedral : 15.421 171.728 1973 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.70 % Allowed : 18.13 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1109 helix: 0.76 (0.20), residues: 721 sheet: -0.70 (1.01), residues: 30 loop : -2.40 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.017 0.002 PHE A 848 TYR 0.016 0.001 TYR A 662 ARG 0.006 0.000 ARG A 959 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2501.91 seconds wall clock time: 45 minutes 57.11 seconds (2757.11 seconds total)