Starting phenix.real_space_refine on Tue Jul 29 18:09:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oxb_17263/07_2025/8oxb_17263.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oxb_17263/07_2025/8oxb_17263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oxb_17263/07_2025/8oxb_17263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oxb_17263/07_2025/8oxb_17263.map" model { file = "/net/cci-nas-00/data/ceres_data/8oxb_17263/07_2025/8oxb_17263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oxb_17263/07_2025/8oxb_17263.cif" } resolution = 2.99 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= 1.000 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: 7 Type Number sf(0) Gaussians V 1 8.30 5 P 1 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 7198 2.51 5 N 1833 2.21 5 O 2049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11137 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8361 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 25, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 2642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2642 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 25, 'TRANS': 302} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'POV': 1, 'VN4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 7.30, per 1000 atoms: 0.66 Number of scatterers: 11137 At special positions: 0 Unit cell: (84.11, 97.7779, 176.631, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 S 54 16.00 P 1 15.00 Mg 1 11.99 O 2049 8.00 N 1833 7.00 C 7198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.04 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG C 1 " - " ASN B 180 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 51.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 118 through 131 removed outlier: 3.630A pdb=" N LEU A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 175 Proline residue: A 147 - end of helix removed outlier: 3.841A pdb=" N THR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.552A pdb=" N GLN A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 331 through 370 removed outlier: 3.605A pdb=" N TYR A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE A 344 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASN A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 380 through 396 removed outlier: 3.965A pdb=" N TRP A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 400 Processing helix chain 'A' and resid 401 through 422 removed outlier: 4.382A pdb=" N TYR A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.911A pdb=" N LEU A 441 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 442 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU A 443 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 521 through 532 removed outlier: 4.145A pdb=" N ARG A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.948A pdb=" N GLY A 544 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 621 through 627 removed outlier: 3.635A pdb=" N GLU A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 662 through 678 removed outlier: 3.592A pdb=" N TRP A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 removed outlier: 3.696A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 735 through 746 Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.588A pdb=" N SER A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.548A pdb=" N ASN A 796 " --> pdb=" O PRO A 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 792 through 796' Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.505A pdb=" N GLU A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 859 removed outlier: 3.507A pdb=" N GLU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.669A pdb=" N ALA A 874 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 904 Processing helix chain 'A' and resid 931 through 938 Processing helix chain 'A' and resid 938 through 963 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 969 through 972 Processing helix chain 'A' and resid 981 through 988 Processing helix chain 'A' and resid 994 through 1001 Processing helix chain 'A' and resid 1008 through 1015 Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.516A pdb=" N GLN A1023 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1057 Proline residue: A1051 - end of helix removed outlier: 4.484A pdb=" N GLN A1057 " --> pdb=" O GLY A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1092 removed outlier: 3.637A pdb=" N GLY A1089 " --> pdb=" O ASN A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1114 removed outlier: 3.538A pdb=" N ILE A1107 " --> pdb=" O ILE A1103 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A1114 " --> pdb=" O TYR A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.726A pdb=" N LEU A1140 " --> pdb=" O ALA A1136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1140' Processing helix chain 'A' and resid 1142 through 1171 Proline residue: A1159 - end of helix Processing helix chain 'A' and resid 1173 through 1181 Processing helix chain 'B' and resid 46 through 74 removed outlier: 3.607A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.911A pdb=" N ILE B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.566A pdb=" N CYS B 94 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 96 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.971A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.816A pdb=" N ARG B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.989A pdb=" N MET B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 243 " --> pdb=" O VAL B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 243' Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.719A pdb=" N ASN B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY B 251 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N PHE B 252 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 253 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 322 through 350 removed outlier: 3.764A pdb=" N GLY B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.505A pdb=" N TRP A 64 " --> pdb=" O CYS A 265 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 278 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY A 277 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.930A pdb=" N GLU A 179 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 305 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER A 217 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N HIS A 307 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP A 211 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.976A pdb=" N TYR A 225 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA5, first strand: chain 'A' and resid 754 through 756 removed outlier: 6.410A pdb=" N THR A 754 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 800 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N CYS A 756 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR A 802 " --> pdb=" O CYS A 756 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG A 797 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE A 864 " --> pdb=" O ARG A 797 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 799 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS A 866 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE A 801 " --> pdb=" O CYS A 866 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE A 728 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N CYS A 865 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 730 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 451 " --> pdb=" O TRP A 729 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 731 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A 453 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 888 " --> pdb=" O ILE A 906 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL A 908 " --> pdb=" O THR A 888 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA A 890 " --> pdb=" O VAL A 908 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 460 through 469 removed outlier: 5.220A pdb=" N ILE A 463 " --> pdb=" O LYS A 709 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 705 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS A 469 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 703 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU A 700 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR A 658 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 702 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 604 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE A 593 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 606 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 608 " --> pdb=" O ASN A 589 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 589 " --> pdb=" O ARG A 608 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR A 578 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.525A pdb=" N ARG B 307 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 118 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU B 275 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET B 120 " --> pdb=" O TYR B 273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 102 through 110 removed outlier: 4.047A pdb=" N CYS B 102 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B 182 " --> pdb=" O THR B 296 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1783 1.31 - 1.43: 3158 1.43 - 1.56: 6353 1.56 - 1.69: 6 1.69 - 1.81: 83 Bond restraints: 11383 Sorted by residual: bond pdb=" C31 POV A1203 " pdb=" O31 POV A1203 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C21 POV A1203 " pdb=" O21 POV A1203 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N POV A1203 " pdb=" C12 POV A1203 " ideal model delta sigma weight residual 1.508 1.465 0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.561 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" N POV A1203 " pdb=" C15 POV A1203 " ideal model delta sigma weight residual 1.491 1.455 0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 11378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 15256 2.27 - 4.53: 143 4.53 - 6.80: 14 6.80 - 9.07: 3 9.07 - 11.33: 1 Bond angle restraints: 15417 Sorted by residual: angle pdb=" O13 POV A1203 " pdb=" P POV A1203 " pdb=" O14 POV A1203 " ideal model delta sigma weight residual 121.11 109.78 11.33 3.00e+00 1.11e-01 1.43e+01 angle pdb=" OG1 THR A1152 " pdb=" CB THR A1152 " pdb=" CG2 THR A1152 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" O11 POV A1203 " pdb=" P POV A1203 " pdb=" O12 POV A1203 " ideal model delta sigma weight residual 97.67 106.62 -8.95 3.00e+00 1.11e-01 8.89e+00 angle pdb=" C32 POV A1203 " pdb=" C31 POV A1203 " pdb=" O31 POV A1203 " ideal model delta sigma weight residual 110.66 119.24 -8.58 3.00e+00 1.11e-01 8.18e+00 angle pdb=" C22 POV A1203 " pdb=" C21 POV A1203 " pdb=" O21 POV A1203 " ideal model delta sigma weight residual 111.03 118.93 -7.90 3.00e+00 1.11e-01 6.93e+00 ... (remaining 15412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 6311 21.52 - 43.04: 446 43.04 - 64.55: 50 64.55 - 86.07: 20 86.07 - 107.59: 4 Dihedral angle restraints: 6831 sinusoidal: 2839 harmonic: 3992 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual -86.00 -130.28 44.28 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.88 107.59 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.01 105.63 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 6828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1466 0.054 - 0.108: 216 0.108 - 0.162: 41 0.162 - 0.216: 2 0.216 - 0.270: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR A 432 " pdb=" CA THR A 432 " pdb=" OG1 THR A 432 " pdb=" CG2 THR A 432 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB THR A1152 " pdb=" CA THR A1152 " pdb=" OG1 THR A1152 " pdb=" CG2 THR A1152 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1723 not shown) Planarity restraints: 1941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 86 " 0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO B 87 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 108 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO A 109 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 792 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 793 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " 0.032 5.00e-02 4.00e+02 ... (remaining 1938 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 130 2.57 - 3.16: 9405 3.16 - 3.74: 17189 3.74 - 4.32: 25217 4.32 - 4.90: 42053 Nonbonded interactions: 93994 Sorted by model distance: nonbonded pdb=" OD2 ASP A 454 " pdb=" O3 VN4 A1201 " model vdw 1.992 3.040 nonbonded pdb=" OH TYR A1055 " pdb=" OG1 THR A1075 " model vdw 1.996 3.040 nonbonded pdb=" OD2 ASP A 454 " pdb="MG MG A1202 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR A 576 " pdb=" O TYR A 588 " model vdw 2.053 3.040 nonbonded pdb=" O HOH A1301 " pdb=" O HOH A1307 " model vdw 2.067 3.040 ... (remaining 93989 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 ========== 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=0.00 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: 1.470 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.004 0.216 11392 Z= 0.248 Angle : 0.581 11.332 15438 Z= 0.280 Chirality : 0.041 0.270 1726 Planarity : 0.005 0.087 1938 Dihedral : 14.734 107.591 4250 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1349 helix: 0.14 (0.22), residues: 598 sheet: -0.22 (0.38), residues: 198 loop : -0.71 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 983 HIS 0.003 0.001 HIS B 283 PHE 0.016 0.001 PHE A 507 TYR 0.011 0.001 TYR B 122 ARG 0.010 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 3) link_NAG-ASN : angle 1.17116 ( 9) link_BETA1-4 : bond 0.01288 ( 2) link_BETA1-4 : angle 2.98265 ( 6) hydrogen bonds : bond 0.25666 ( 504) hydrogen bonds : angle 8.59483 ( 1428) SS BOND : bond 0.00317 ( 3) SS BOND : angle 1.31558 ( 6) covalent geometry : bond 0.00320 (11383) covalent geometry : angle 0.57667 (15417) Misc. bond : bond 0.21578 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.311 Fit side-chains REVERT: A 538 MET cc_start: 0.8273 (mtm) cc_final: 0.7725 (mtp) REVERT: A 608 ARG cc_start: 0.7438 (ttt90) cc_final: 0.7079 (ttm-80) REVERT: B 215 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7018 (mtm110) outliers start: 0 outliers final: 1 residues processed: 143 average time/residue: 1.1071 time to fit residues: 173.0654 Evaluate side-chains 107 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.1980 chunk 40 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 442 ASN A 447 GLN A 549 GLN A 872 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.179783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128774 restraints weight = 12495.283| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.42 r_work: 0.3476 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11392 Z= 0.134 Angle : 0.604 10.281 15438 Z= 0.311 Chirality : 0.043 0.245 1726 Planarity : 0.005 0.065 1938 Dihedral : 8.413 68.651 1636 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.42 % Allowed : 8.52 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.23), residues: 1349 helix: 0.70 (0.21), residues: 633 sheet: 0.40 (0.38), residues: 193 loop : -0.80 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.033 0.001 PHE A 666 TYR 0.021 0.002 TYR B 273 ARG 0.007 0.001 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 3) link_NAG-ASN : angle 1.45806 ( 9) link_BETA1-4 : bond 0.01393 ( 2) link_BETA1-4 : angle 2.56382 ( 6) hydrogen bonds : bond 0.04883 ( 504) hydrogen bonds : angle 5.41303 ( 1428) SS BOND : bond 0.00299 ( 3) SS BOND : angle 0.73625 ( 6) covalent geometry : bond 0.00301 (11383) covalent geometry : angle 0.60141 (15417) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 2.129 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7891 (ptpt) cc_final: 0.7175 (pptt) REVERT: A 110 MET cc_start: 0.5893 (tmm) cc_final: 0.5613 (tmm) REVERT: A 113 PHE cc_start: 0.6649 (m-80) cc_final: 0.5932 (t80) REVERT: A 247 ASP cc_start: 0.8208 (t0) cc_final: 0.7999 (t0) REVERT: A 289 ASP cc_start: 0.7678 (m-30) cc_final: 0.7379 (m-30) REVERT: A 538 MET cc_start: 0.8360 (mtm) cc_final: 0.7752 (mtp) REVERT: A 608 ARG cc_start: 0.7546 (ttt90) cc_final: 0.7035 (ttm-80) REVERT: A 851 LYS cc_start: 0.7230 (tptt) cc_final: 0.6946 (tmtt) REVERT: A 980 TYR cc_start: 0.8865 (m-80) cc_final: 0.8587 (m-80) REVERT: A 1055 TYR cc_start: 0.7273 (m-80) cc_final: 0.6688 (m-80) REVERT: A 1179 GLN cc_start: 0.5659 (OUTLIER) cc_final: 0.4903 (mm110) REVERT: B 215 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7294 (mtm110) REVERT: B 246 ASP cc_start: 0.6998 (m-30) cc_final: 0.6632 (t0) REVERT: B 261 MET cc_start: 0.8703 (mmm) cc_final: 0.8475 (mmm) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 1.2695 time to fit residues: 186.6243 Evaluate side-chains 115 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 302 ASN A 479 HIS B 211 ASN B 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.172038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123918 restraints weight = 12737.920| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.26 r_work: 0.3422 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11392 Z= 0.204 Angle : 0.612 11.087 15438 Z= 0.311 Chirality : 0.045 0.247 1726 Planarity : 0.005 0.057 1938 Dihedral : 7.614 73.338 1632 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.26 % Allowed : 11.78 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1349 helix: 0.79 (0.21), residues: 633 sheet: 0.39 (0.38), residues: 193 loop : -0.86 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.027 0.002 PHE A 666 TYR 0.015 0.002 TYR B 122 ARG 0.006 0.000 ARG A 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 1.77807 ( 9) link_BETA1-4 : bond 0.01787 ( 2) link_BETA1-4 : angle 3.06835 ( 6) hydrogen bonds : bond 0.04716 ( 504) hydrogen bonds : angle 5.14457 ( 1428) SS BOND : bond 0.00165 ( 3) SS BOND : angle 0.70019 ( 6) covalent geometry : bond 0.00500 (11383) covalent geometry : angle 0.60781 (15417) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.664 Fit side-chains REVERT: A 110 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5932 (tmm) REVERT: A 113 PHE cc_start: 0.6870 (m-80) cc_final: 0.5993 (t80) REVERT: A 479 HIS cc_start: 0.7431 (m90) cc_final: 0.6791 (m90) REVERT: A 538 MET cc_start: 0.8511 (mtm) cc_final: 0.7949 (mtp) REVERT: A 608 ARG cc_start: 0.7573 (ttt90) cc_final: 0.6987 (ttm-80) REVERT: A 734 ASP cc_start: 0.8246 (m-30) cc_final: 0.7989 (m-30) REVERT: A 1055 TYR cc_start: 0.7395 (m-80) cc_final: 0.6681 (m-80) REVERT: A 1179 GLN cc_start: 0.5780 (OUTLIER) cc_final: 0.5057 (mm110) REVERT: B 55 PHE cc_start: 0.7743 (m-10) cc_final: 0.7536 (m-10) REVERT: B 121 TYR cc_start: 0.8856 (m-80) cc_final: 0.8624 (m-80) REVERT: B 211 ASN cc_start: 0.8585 (m110) cc_final: 0.8287 (m110) REVERT: B 215 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7538 (mtm110) REVERT: B 246 ASP cc_start: 0.6970 (m-30) cc_final: 0.6557 (t0) outliers start: 27 outliers final: 9 residues processed: 128 average time/residue: 2.0133 time to fit residues: 288.1795 Evaluate side-chains 117 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A1023 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.175151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125765 restraints weight = 12561.540| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.34 r_work: 0.3445 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11392 Z= 0.137 Angle : 0.559 11.489 15438 Z= 0.284 Chirality : 0.042 0.260 1726 Planarity : 0.004 0.058 1938 Dihedral : 6.932 72.825 1632 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.42 % Allowed : 12.78 % 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 (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: 0.27 (0.24), residues: 1349 helix: 0.97 (0.21), residues: 635 sheet: 0.39 (0.38), residues: 191 loop : -0.82 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.032 0.001 PHE A 666 TYR 0.014 0.001 TYR A 405 ARG 0.004 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 3) link_NAG-ASN : angle 1.63954 ( 9) link_BETA1-4 : bond 0.01787 ( 2) link_BETA1-4 : angle 3.00045 ( 6) hydrogen bonds : bond 0.03903 ( 504) hydrogen bonds : angle 4.76729 ( 1428) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.62659 ( 6) covalent geometry : bond 0.00322 (11383) covalent geometry : angle 0.55518 (15417) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.066 Fit side-chains REVERT: A 110 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5849 (tmm) REVERT: A 113 PHE cc_start: 0.6600 (m-80) cc_final: 0.5929 (t80) REVERT: A 289 ASP cc_start: 0.7693 (m-30) cc_final: 0.7423 (m-30) REVERT: A 432 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8534 (p) REVERT: A 479 HIS cc_start: 0.7361 (m90) cc_final: 0.6755 (m90) REVERT: A 538 MET cc_start: 0.8230 (mtm) cc_final: 0.7613 (mtp) REVERT: A 569 PHE cc_start: 0.7915 (t80) cc_final: 0.7676 (t80) REVERT: A 608 ARG cc_start: 0.7561 (ttt90) cc_final: 0.6991 (ttm-80) REVERT: A 851 LYS cc_start: 0.7236 (tptt) cc_final: 0.6939 (tptm) REVERT: A 898 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 980 TYR cc_start: 0.8897 (m-80) cc_final: 0.8666 (m-80) REVERT: A 1097 PHE cc_start: 0.7910 (t80) cc_final: 0.7703 (t80) REVERT: A 1179 GLN cc_start: 0.5729 (OUTLIER) cc_final: 0.4962 (mm110) REVERT: B 121 TYR cc_start: 0.8593 (m-80) cc_final: 0.8370 (m-80) REVERT: B 215 ARG cc_start: 0.7811 (mtm110) cc_final: 0.7227 (mtm110) REVERT: B 244 ASP cc_start: 0.8180 (t0) cc_final: 0.7784 (m-30) REVERT: B 246 ASP cc_start: 0.6910 (m-30) cc_final: 0.6556 (t0) REVERT: B 249 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7471 (t0) outliers start: 29 outliers final: 10 residues processed: 140 average time/residue: 1.0565 time to fit residues: 165.9852 Evaluate side-chains 126 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.172406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122863 restraints weight = 12652.930| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.33 r_work: 0.3398 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11392 Z= 0.198 Angle : 0.609 13.961 15438 Z= 0.305 Chirality : 0.044 0.257 1726 Planarity : 0.005 0.058 1938 Dihedral : 6.961 76.067 1632 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.42 % Allowed : 14.62 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1349 helix: 0.95 (0.21), residues: 628 sheet: 0.29 (0.38), residues: 192 loop : -0.85 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 260 HIS 0.004 0.001 HIS A 449 PHE 0.025 0.002 PHE A 666 TYR 0.015 0.002 TYR B 122 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00131 ( 3) link_NAG-ASN : angle 1.73601 ( 9) link_BETA1-4 : bond 0.01716 ( 2) link_BETA1-4 : angle 3.19147 ( 6) hydrogen bonds : bond 0.04161 ( 504) hydrogen bonds : angle 4.80839 ( 1428) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.70711 ( 6) covalent geometry : bond 0.00484 (11383) covalent geometry : angle 0.60424 (15417) Misc. bond : bond 0.00178 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.167 Fit side-chains REVERT: A 110 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5773 (tmm) REVERT: A 244 GLU cc_start: 0.7310 (tp30) cc_final: 0.7107 (tp30) REVERT: A 289 ASP cc_start: 0.7910 (m-30) cc_final: 0.7643 (m-30) REVERT: A 479 HIS cc_start: 0.7450 (m90) cc_final: 0.6769 (m90) REVERT: A 538 MET cc_start: 0.8419 (mtm) cc_final: 0.7892 (mtp) REVERT: A 569 PHE cc_start: 0.8003 (t80) cc_final: 0.7693 (t80) REVERT: A 608 ARG cc_start: 0.7660 (ttt90) cc_final: 0.7234 (ttm-80) REVERT: A 734 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: A 845 LYS cc_start: 0.7596 (mppt) cc_final: 0.7291 (mppt) REVERT: A 1045 MET cc_start: 0.8230 (mtm) cc_final: 0.7878 (mtt) REVERT: A 1179 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5031 (mm110) REVERT: B 121 TYR cc_start: 0.8777 (m-80) cc_final: 0.8549 (m-80) REVERT: B 155 LYS cc_start: 0.6778 (mmpt) cc_final: 0.6285 (tmmm) REVERT: B 215 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7429 (mtm110) REVERT: B 244 ASP cc_start: 0.8249 (t0) cc_final: 0.7691 (m-30) REVERT: B 246 ASP cc_start: 0.6938 (m-30) cc_final: 0.6512 (t0) REVERT: B 249 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7387 (t0) outliers start: 29 outliers final: 15 residues processed: 131 average time/residue: 0.9182 time to fit residues: 134.1165 Evaluate side-chains 130 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.176625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124835 restraints weight = 12576.393| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.45 r_work: 0.3423 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11392 Z= 0.125 Angle : 0.565 13.419 15438 Z= 0.282 Chirality : 0.042 0.258 1726 Planarity : 0.004 0.057 1938 Dihedral : 6.714 74.586 1632 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.42 % Allowed : 15.96 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1349 helix: 1.13 (0.22), residues: 628 sheet: 0.45 (0.39), residues: 188 loop : -0.85 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 260 HIS 0.003 0.001 HIS A 359 PHE 0.021 0.001 PHE A 666 TYR 0.013 0.001 TYR A 405 ARG 0.006 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 3) link_NAG-ASN : angle 1.59328 ( 9) link_BETA1-4 : bond 0.01664 ( 2) link_BETA1-4 : angle 2.96935 ( 6) hydrogen bonds : bond 0.03698 ( 504) hydrogen bonds : angle 4.58110 ( 1428) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.60701 ( 6) covalent geometry : bond 0.00289 (11383) covalent geometry : angle 0.56101 (15417) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5746 (tmm) REVERT: A 241 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6709 (tpt) REVERT: A 289 ASP cc_start: 0.7682 (m-30) cc_final: 0.7393 (m-30) REVERT: A 479 HIS cc_start: 0.7351 (m90) cc_final: 0.6721 (m90) REVERT: A 569 PHE cc_start: 0.7875 (t80) cc_final: 0.7629 (t80) REVERT: A 608 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7129 (ttm-80) REVERT: A 734 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: A 759 GLU cc_start: 0.7874 (tp30) cc_final: 0.7652 (tp30) REVERT: A 851 LYS cc_start: 0.7296 (tptt) cc_final: 0.6900 (tptp) REVERT: A 1045 MET cc_start: 0.8073 (mtm) cc_final: 0.7719 (mtt) REVERT: A 1097 PHE cc_start: 0.7932 (t80) cc_final: 0.7699 (t80) REVERT: A 1179 GLN cc_start: 0.5708 (OUTLIER) cc_final: 0.4939 (mm110) REVERT: B 155 LYS cc_start: 0.6844 (mmpt) cc_final: 0.6246 (tmmm) REVERT: B 215 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7191 (mtm110) REVERT: B 244 ASP cc_start: 0.8168 (t0) cc_final: 0.7711 (m-30) REVERT: B 246 ASP cc_start: 0.6894 (m-30) cc_final: 0.6559 (t0) REVERT: B 249 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7498 (t0) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 1.0182 time to fit residues: 149.7399 Evaluate side-chains 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 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 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.169598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120943 restraints weight = 12776.171| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.29 r_work: 0.3379 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11392 Z= 0.224 Angle : 0.632 12.430 15438 Z= 0.317 Chirality : 0.045 0.255 1726 Planarity : 0.005 0.058 1938 Dihedral : 6.949 76.905 1632 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.76 % Allowed : 17.13 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1349 helix: 0.93 (0.21), residues: 628 sheet: 0.27 (0.39), residues: 190 loop : -0.91 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1171 HIS 0.003 0.001 HIS A 449 PHE 0.020 0.002 PHE A 666 TYR 0.016 0.002 TYR B 122 ARG 0.004 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 1.78211 ( 9) link_BETA1-4 : bond 0.01656 ( 2) link_BETA1-4 : angle 3.20372 ( 6) hydrogen bonds : bond 0.04178 ( 504) hydrogen bonds : angle 4.76926 ( 1428) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.76342 ( 6) covalent geometry : bond 0.00547 (11383) covalent geometry : angle 0.62758 (15417) Misc. bond : bond 0.00204 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7295 (pptt) REVERT: A 110 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5892 (tmm) REVERT: A 169 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6501 (ptp) REVERT: A 241 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.6855 (tpt) REVERT: A 289 ASP cc_start: 0.7915 (m-30) cc_final: 0.7645 (m-30) REVERT: A 479 HIS cc_start: 0.7442 (m90) cc_final: 0.6777 (m90) REVERT: A 538 MET cc_start: 0.8765 (mtm) cc_final: 0.8369 (mtp) REVERT: A 569 PHE cc_start: 0.8056 (t80) cc_final: 0.7832 (t80) REVERT: A 608 ARG cc_start: 0.7866 (ttt90) cc_final: 0.7291 (ttm-80) REVERT: A 845 LYS cc_start: 0.7635 (mppt) cc_final: 0.7324 (mppt) REVERT: A 1045 MET cc_start: 0.8290 (mtm) cc_final: 0.7881 (mtt) REVERT: A 1179 GLN cc_start: 0.5853 (OUTLIER) cc_final: 0.5104 (mm110) REVERT: B 155 LYS cc_start: 0.6949 (mmpt) cc_final: 0.6315 (tmmm) REVERT: B 166 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6539 (ptmt) REVERT: B 215 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7442 (mtm110) REVERT: B 244 ASP cc_start: 0.8233 (t0) cc_final: 0.7724 (m-30) REVERT: B 246 ASP cc_start: 0.7022 (m-30) cc_final: 0.6610 (t0) REVERT: B 249 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7731 (t0) outliers start: 33 outliers final: 19 residues processed: 132 average time/residue: 1.0247 time to fit residues: 149.2046 Evaluate side-chains 132 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.176152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124411 restraints weight = 12676.501| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.46 r_work: 0.3420 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11392 Z= 0.120 Angle : 0.581 13.246 15438 Z= 0.288 Chirality : 0.042 0.258 1726 Planarity : 0.004 0.057 1938 Dihedral : 6.666 74.805 1632 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.51 % Allowed : 17.54 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1349 helix: 1.11 (0.21), residues: 628 sheet: 0.37 (0.39), residues: 192 loop : -0.84 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.021 0.001 PHE A 529 TYR 0.015 0.001 TYR A 405 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 3) link_NAG-ASN : angle 1.59107 ( 9) link_BETA1-4 : bond 0.01561 ( 2) link_BETA1-4 : angle 2.86191 ( 6) hydrogen bonds : bond 0.03611 ( 504) hydrogen bonds : angle 4.55831 ( 1428) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.62168 ( 6) covalent geometry : bond 0.00280 (11383) covalent geometry : angle 0.57739 (15417) Misc. bond : bond 0.00104 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5756 (tmm) REVERT: A 169 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6312 (ptp) REVERT: A 241 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6754 (tpt) REVERT: A 248 GLN cc_start: 0.8178 (pt0) cc_final: 0.7754 (pt0) REVERT: A 289 ASP cc_start: 0.7683 (m-30) cc_final: 0.7408 (m-30) REVERT: A 479 HIS cc_start: 0.7363 (m90) cc_final: 0.6727 (m90) REVERT: A 538 MET cc_start: 0.8546 (mtm) cc_final: 0.8160 (mtp) REVERT: A 569 PHE cc_start: 0.7844 (t80) cc_final: 0.7608 (t80) REVERT: A 608 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7414 (ttm-80) REVERT: A 759 GLU cc_start: 0.7884 (tp30) cc_final: 0.7665 (tp30) REVERT: A 845 LYS cc_start: 0.7615 (mppt) cc_final: 0.7300 (mppt) REVERT: A 851 LYS cc_start: 0.7307 (tptt) cc_final: 0.6906 (tptp) REVERT: A 1045 MET cc_start: 0.8097 (mtm) cc_final: 0.7743 (mtt) REVERT: A 1097 PHE cc_start: 0.7937 (t80) cc_final: 0.7691 (t80) REVERT: A 1179 GLN cc_start: 0.5786 (OUTLIER) cc_final: 0.5016 (mm110) REVERT: B 155 LYS cc_start: 0.6839 (mmpt) cc_final: 0.6224 (tmmm) REVERT: B 215 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7201 (mtm110) REVERT: B 244 ASP cc_start: 0.8138 (t0) cc_final: 0.7678 (m-30) REVERT: B 246 ASP cc_start: 0.6891 (m-30) cc_final: 0.6548 (t0) REVERT: B 249 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7516 (t0) outliers start: 30 outliers final: 16 residues processed: 129 average time/residue: 1.0446 time to fit residues: 148.9036 Evaluate side-chains 129 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 GLN Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.175888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.124002 restraints weight = 12643.611| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.45 r_work: 0.3417 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11392 Z= 0.140 Angle : 0.599 13.130 15438 Z= 0.295 Chirality : 0.042 0.258 1726 Planarity : 0.004 0.059 1938 Dihedral : 6.581 75.287 1632 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.34 % Allowed : 18.05 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1349 helix: 1.12 (0.21), residues: 626 sheet: 0.37 (0.39), residues: 192 loop : -0.83 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1171 HIS 0.003 0.001 HIS A 359 PHE 0.037 0.001 PHE A 666 TYR 0.014 0.001 TYR A 405 ARG 0.006 0.000 ARG B 262 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 1.64296 ( 9) link_BETA1-4 : bond 0.01504 ( 2) link_BETA1-4 : angle 2.88133 ( 6) hydrogen bonds : bond 0.03680 ( 504) hydrogen bonds : angle 4.56556 ( 1428) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.63039 ( 6) covalent geometry : bond 0.00335 (11383) covalent geometry : angle 0.59481 (15417) Misc. bond : bond 0.00121 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5869 (tmm) REVERT: A 169 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6318 (ptp) REVERT: A 241 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.6690 (tpt) REVERT: A 289 ASP cc_start: 0.7682 (m-30) cc_final: 0.7407 (m-30) REVERT: A 479 HIS cc_start: 0.7370 (m90) cc_final: 0.6729 (m90) REVERT: A 538 MET cc_start: 0.8583 (mtm) cc_final: 0.8221 (mtp) REVERT: A 569 PHE cc_start: 0.7818 (t80) cc_final: 0.7581 (t80) REVERT: A 608 ARG cc_start: 0.7740 (ttt90) cc_final: 0.7277 (ttm-80) REVERT: A 759 GLU cc_start: 0.7892 (tp30) cc_final: 0.7667 (tp30) REVERT: A 845 LYS cc_start: 0.7616 (mppt) cc_final: 0.7303 (mppt) REVERT: A 851 LYS cc_start: 0.7283 (tptt) cc_final: 0.6892 (tptp) REVERT: A 1045 MET cc_start: 0.8094 (mtm) cc_final: 0.7737 (mtt) REVERT: A 1097 PHE cc_start: 0.7926 (t80) cc_final: 0.7670 (t80) REVERT: B 155 LYS cc_start: 0.6842 (mmpt) cc_final: 0.6221 (tmmm) REVERT: B 166 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6377 (ptmt) REVERT: B 215 ARG cc_start: 0.7817 (mtm110) cc_final: 0.7203 (mtm110) REVERT: B 244 ASP cc_start: 0.8199 (t0) cc_final: 0.7663 (m-30) REVERT: B 246 ASP cc_start: 0.6909 (m-30) cc_final: 0.6566 (t0) REVERT: B 249 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.7397 (t0) outliers start: 28 outliers final: 17 residues processed: 132 average time/residue: 0.9666 time to fit residues: 141.3155 Evaluate side-chains 128 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.176851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125278 restraints weight = 12559.441| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.44 r_work: 0.3431 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11392 Z= 0.125 Angle : 0.590 13.125 15438 Z= 0.291 Chirality : 0.042 0.259 1726 Planarity : 0.004 0.058 1938 Dihedral : 6.450 74.647 1632 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.92 % Allowed : 18.71 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1349 helix: 1.21 (0.22), residues: 626 sheet: 0.38 (0.39), residues: 192 loop : -0.81 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.030 0.001 PHE A 666 TYR 0.013 0.001 TYR A 405 ARG 0.006 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 3) link_NAG-ASN : angle 1.63836 ( 9) link_BETA1-4 : bond 0.01495 ( 2) link_BETA1-4 : angle 2.79734 ( 6) hydrogen bonds : bond 0.03556 ( 504) hydrogen bonds : angle 4.49004 ( 1428) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.61404 ( 6) covalent geometry : bond 0.00293 (11383) covalent geometry : angle 0.58629 (15417) Misc. bond : bond 0.00092 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5862 (tmm) REVERT: A 169 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6338 (ptp) REVERT: A 241 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.6737 (tpt) REVERT: A 289 ASP cc_start: 0.7618 (m-30) cc_final: 0.7322 (m-30) REVERT: A 479 HIS cc_start: 0.7452 (m90) cc_final: 0.6761 (m90) REVERT: A 538 MET cc_start: 0.8581 (mtm) cc_final: 0.8222 (mtp) REVERT: A 569 PHE cc_start: 0.7807 (t80) cc_final: 0.7540 (t80) REVERT: A 608 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7451 (ttm-80) REVERT: A 734 ASP cc_start: 0.8192 (m-30) cc_final: 0.7820 (m-30) REVERT: A 759 GLU cc_start: 0.7881 (tp30) cc_final: 0.7674 (tp30) REVERT: A 845 LYS cc_start: 0.7615 (mppt) cc_final: 0.7303 (mppt) REVERT: A 851 LYS cc_start: 0.7307 (tptt) cc_final: 0.6908 (tptp) REVERT: A 1000 MET cc_start: 0.7970 (tmm) cc_final: 0.7761 (ttt) REVERT: A 1045 MET cc_start: 0.8075 (mtm) cc_final: 0.7717 (mtt) REVERT: B 155 LYS cc_start: 0.6839 (mmpt) cc_final: 0.6217 (tmmm) REVERT: B 166 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.6469 (ptmt) REVERT: B 215 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7235 (mtm110) REVERT: B 244 ASP cc_start: 0.8146 (t0) cc_final: 0.7637 (m-30) REVERT: B 246 ASP cc_start: 0.6929 (m-30) cc_final: 0.6606 (t0) REVERT: B 249 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7299 (t0) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 1.1511 time to fit residues: 164.1791 Evaluate side-chains 133 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 249 ASN Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122963 restraints weight = 12598.877| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.46 r_work: 0.3399 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11392 Z= 0.162 Angle : 0.612 13.144 15438 Z= 0.303 Chirality : 0.043 0.257 1726 Planarity : 0.005 0.058 1938 Dihedral : 6.528 76.178 1632 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.01 % Allowed : 18.55 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1349 helix: 1.13 (0.21), residues: 626 sheet: 0.41 (0.39), residues: 190 loop : -0.79 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1171 HIS 0.003 0.001 HIS A 167 PHE 0.044 0.002 PHE A1097 TYR 0.014 0.001 TYR A 100 ARG 0.006 0.000 ARG A 628 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 3) link_NAG-ASN : angle 1.70491 ( 9) link_BETA1-4 : bond 0.01416 ( 2) link_BETA1-4 : angle 2.82668 ( 6) hydrogen bonds : bond 0.03790 ( 504) hydrogen bonds : angle 4.55228 ( 1428) SS BOND : bond 0.00240 ( 3) SS BOND : angle 0.70650 ( 6) covalent geometry : bond 0.00391 (11383) covalent geometry : angle 0.60786 (15417) Misc. bond : bond 0.00143 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7451.41 seconds wall clock time: 133 minutes 47.20 seconds (8027.20 seconds total)