Starting phenix.real_space_refine on Sat Nov 16 17:11:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/11_2024/8oxb_17263.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/11_2024/8oxb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/11_2024/8oxb_17263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/11_2024/8oxb_17263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/11_2024/8oxb_17263.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxb_17263/11_2024/8oxb_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.08, per 1000 atoms: 0.64 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: 3.33 Conformation dependent library (CDL) restraints added in 1.5 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: 1.66 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: 4.02 Time building geometry restraints manager: 3.60 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: 0.700 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- 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 : 0.003 0.072 11383 Z= 0.207 Angle : 0.577 11.332 15417 Z= 0.279 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 *********************** 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 : 1.356 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: 1.1608 time to fit residues: 181.3835 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 : 1.418 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11383 Z= 0.193 Angle : 0.601 10.307 15417 Z= 0.310 Chirality : 0.043 0.245 1726 Planarity : 0.005 0.065 1938 Dihedral : 8.419 68.596 1636 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.42 % Allowed : 8.60 % Favored : 89.97 % 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: 0.69 (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 *********************** 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 : 1.198 Fit side-chains revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7404 (pptt) REVERT: A 110 MET cc_start: 0.5895 (tmm) cc_final: 0.5644 (tmm) REVERT: A 113 PHE cc_start: 0.6345 (m-80) cc_final: 0.5980 (t80) REVERT: A 289 ASP cc_start: 0.7325 (m-30) cc_final: 0.7080 (m-30) REVERT: A 538 MET cc_start: 0.8177 (mtm) cc_final: 0.7586 (mtp) REVERT: A 608 ARG cc_start: 0.7370 (ttt90) cc_final: 0.6849 (ttm-80) REVERT: A 851 LYS cc_start: 0.7330 (tptt) cc_final: 0.7066 (tmtt) REVERT: A 980 TYR cc_start: 0.8747 (m-80) cc_final: 0.8523 (m-80) REVERT: A 1055 TYR cc_start: 0.7105 (m-80) cc_final: 0.6652 (m-80) REVERT: A 1179 GLN cc_start: 0.5775 (OUTLIER) cc_final: 0.4900 (mm110) REVERT: B 215 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7160 (mtm110) REVERT: B 261 MET cc_start: 0.8644 (mmm) cc_final: 0.8345 (mmm) outliers start: 17 outliers final: 7 residues processed: 133 average time/residue: 1.0493 time to fit residues: 154.5945 Evaluate side-chains 117 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 68 optimal weight: 9.9990 chunk 38 optimal weight: 0.0030 chunk 102 optimal weight: 0.0570 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.5108 ------------------------------------------------------------------------------- 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 B 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11383 Z= 0.176 Angle : 0.548 10.897 15417 Z= 0.280 Chirality : 0.042 0.253 1726 Planarity : 0.005 0.057 1938 Dihedral : 7.234 73.234 1632 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.09 % Allowed : 10.94 % Favored : 86.97 % 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: 0.36 (0.24), residues: 1349 helix: 1.01 (0.21), residues: 637 sheet: 0.50 (0.39), residues: 193 loop : -0.75 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.024 0.001 PHE A 666 TYR 0.013 0.001 TYR B 273 ARG 0.006 0.000 ARG A 271 *********************** 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 155 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 1.283 Fit side-chains REVERT: A 107 PHE cc_start: 0.7122 (t80) cc_final: 0.6745 (t80) REVERT: A 110 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5857 (tmm) REVERT: A 113 PHE cc_start: 0.6225 (m-80) cc_final: 0.5968 (t80) REVERT: A 289 ASP cc_start: 0.7304 (m-30) cc_final: 0.7068 (m-30) REVERT: A 479 HIS cc_start: 0.7262 (m-70) cc_final: 0.6746 (m90) REVERT: A 538 MET cc_start: 0.8094 (mtm) cc_final: 0.7615 (mtp) REVERT: A 608 ARG cc_start: 0.7353 (ttt90) cc_final: 0.6810 (ttm-80) REVERT: A 641 ASP cc_start: 0.8119 (m-30) cc_final: 0.7893 (m-30) REVERT: A 734 ASP cc_start: 0.8023 (m-30) cc_final: 0.7726 (m-30) REVERT: A 898 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8038 (p) REVERT: A 1179 GLN cc_start: 0.5773 (OUTLIER) cc_final: 0.4855 (mm110) REVERT: B 215 ARG cc_start: 0.7568 (mtm110) cc_final: 0.7165 (mtm110) REVERT: B 244 ASP cc_start: 0.7946 (t0) cc_final: 0.7646 (m-30) REVERT: B 250 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7506 (p0) REVERT: B 261 MET cc_start: 0.8628 (mmm) cc_final: 0.8409 (mmt) outliers start: 25 outliers final: 7 residues processed: 145 average time/residue: 0.9959 time to fit residues: 160.3165 Evaluate side-chains 122 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 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 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 121 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11383 Z= 0.220 Angle : 0.560 11.284 15417 Z= 0.285 Chirality : 0.043 0.261 1726 Planarity : 0.005 0.057 1938 Dihedral : 6.904 74.968 1632 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.42 % Allowed : 12.20 % Favored : 85.38 % 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: 0.42 (0.24), residues: 1349 helix: 1.11 (0.21), residues: 638 sheet: 0.48 (0.39), residues: 193 loop : -0.79 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.033 0.001 PHE A 666 TYR 0.011 0.001 TYR B 122 ARG 0.006 0.000 ARG B 37 *********************** 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 149 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.334 Fit side-chains REVERT: A 110 MET cc_start: 0.6183 (OUTLIER) cc_final: 0.5916 (tmm) REVERT: A 113 PHE cc_start: 0.6227 (m-80) cc_final: 0.5975 (t80) REVERT: A 289 ASP cc_start: 0.7275 (m-30) cc_final: 0.7054 (m-30) REVERT: A 479 HIS cc_start: 0.7236 (m90) cc_final: 0.6693 (m90) REVERT: A 608 ARG cc_start: 0.7400 (ttt90) cc_final: 0.6847 (ttm-80) REVERT: A 641 ASP cc_start: 0.7991 (m-30) cc_final: 0.7608 (m-30) REVERT: A 734 ASP cc_start: 0.7994 (m-30) cc_final: 0.7709 (m-30) REVERT: A 851 LYS cc_start: 0.7365 (tptt) cc_final: 0.7069 (tptm) REVERT: A 898 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8077 (p) REVERT: A 1179 GLN cc_start: 0.5799 (OUTLIER) cc_final: 0.4874 (mm110) REVERT: B 121 TYR cc_start: 0.8376 (m-80) cc_final: 0.8163 (m-80) REVERT: B 215 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7147 (mtm110) REVERT: B 244 ASP cc_start: 0.8027 (t0) cc_final: 0.7613 (m-30) REVERT: B 249 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7568 (t0) REVERT: B 250 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7465 (p0) REVERT: B 261 MET cc_start: 0.8656 (mmm) cc_final: 0.8436 (mmm) outliers start: 29 outliers final: 9 residues processed: 135 average time/residue: 0.9702 time to fit residues: 146.6450 Evaluate side-chains 123 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 898 VAL 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 91 CYS 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 108 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 0.0370 chunk 32 optimal weight: 0.3980 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11383 Z= 0.164 Angle : 0.549 15.182 15417 Z= 0.275 Chirality : 0.042 0.261 1726 Planarity : 0.004 0.056 1938 Dihedral : 6.736 75.443 1632 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.84 % Allowed : 14.45 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.24), residues: 1349 helix: 1.22 (0.21), residues: 638 sheet: 0.58 (0.39), residues: 190 loop : -0.78 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 260 HIS 0.003 0.001 HIS B 283 PHE 0.024 0.001 PHE A 666 TYR 0.014 0.001 TYR A 100 ARG 0.006 0.000 ARG B 37 *********************** 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 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 1.295 Fit side-chains REVERT: A 110 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5881 (tmm) REVERT: A 113 PHE cc_start: 0.6214 (m-80) cc_final: 0.5985 (t80) REVERT: A 289 ASP cc_start: 0.7183 (m-30) cc_final: 0.6941 (m-30) REVERT: A 479 HIS cc_start: 0.7219 (m90) cc_final: 0.6667 (m90) REVERT: A 608 ARG cc_start: 0.7507 (ttt90) cc_final: 0.6944 (ttm-80) REVERT: A 641 ASP cc_start: 0.8036 (m-30) cc_final: 0.7748 (m-30) REVERT: A 734 ASP cc_start: 0.7971 (m-30) cc_final: 0.7677 (m-30) REVERT: A 851 LYS cc_start: 0.7244 (tptt) cc_final: 0.6929 (tptm) REVERT: A 1179 GLN cc_start: 0.5784 (OUTLIER) cc_final: 0.4859 (mm110) REVERT: B 121 TYR cc_start: 0.8312 (m-80) cc_final: 0.8085 (m-80) REVERT: B 188 ILE cc_start: 0.6952 (mm) cc_final: 0.6717 (mt) REVERT: B 215 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7122 (mtm110) REVERT: B 244 ASP cc_start: 0.8004 (t0) cc_final: 0.7589 (m-30) REVERT: B 250 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7462 (p0) REVERT: B 261 MET cc_start: 0.8668 (mmm) cc_final: 0.8457 (mmt) REVERT: B 273 TYR cc_start: 0.7856 (t80) cc_final: 0.7538 (t80) outliers start: 22 outliers final: 9 residues processed: 125 average time/residue: 1.0201 time to fit residues: 141.7921 Evaluate side-chains 121 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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 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 250 ASN Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 11383 Z= 0.479 Angle : 0.689 12.183 15417 Z= 0.349 Chirality : 0.048 0.254 1726 Planarity : 0.005 0.059 1938 Dihedral : 7.285 77.995 1632 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 15.54 % Favored : 82.21 % 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: -0.00 (0.23), residues: 1349 helix: 0.77 (0.21), residues: 627 sheet: 0.16 (0.38), residues: 195 loop : -0.92 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 260 HIS 0.004 0.001 HIS A 74 PHE 0.024 0.002 PHE A 666 TYR 0.023 0.002 TYR B 122 ARG 0.004 0.001 ARG A 628 *********************** 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 137 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.423 Fit side-chains REVERT: A 72 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7612 (pptt) REVERT: A 110 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6105 (tmm) REVERT: A 289 ASP cc_start: 0.7363 (m-30) cc_final: 0.7132 (m-30) REVERT: A 479 HIS cc_start: 0.7216 (m90) cc_final: 0.6666 (m90) REVERT: A 608 ARG cc_start: 0.7568 (ttt90) cc_final: 0.6966 (ttm-80) REVERT: A 641 ASP cc_start: 0.8133 (m-30) cc_final: 0.7805 (m-30) REVERT: A 845 LYS cc_start: 0.7827 (mppt) cc_final: 0.7484 (mppt) REVERT: A 1045 MET cc_start: 0.7835 (mtm) cc_final: 0.7426 (mtt) REVERT: A 1179 GLN cc_start: 0.5979 (OUTLIER) cc_final: 0.5057 (mm110) REVERT: B 155 LYS cc_start: 0.6614 (mmpt) cc_final: 0.6290 (tmmm) REVERT: B 188 ILE cc_start: 0.6988 (mm) cc_final: 0.6759 (mt) REVERT: B 215 ARG cc_start: 0.7525 (mtm110) cc_final: 0.7115 (mtm110) REVERT: B 244 ASP cc_start: 0.8010 (t0) cc_final: 0.7679 (m-30) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.9962 time to fit residues: 140.5137 Evaluate side-chains 125 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 255 THR Chi-restraints excluded: chain A residue 333 ILE 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 1058 THR 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 250 ASN Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A1039 HIS B 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11383 Z= 0.204 Angle : 0.574 12.737 15417 Z= 0.288 Chirality : 0.042 0.254 1726 Planarity : 0.004 0.058 1938 Dihedral : 6.781 74.678 1632 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 17.21 % Favored : 80.95 % 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: 0.30 (0.24), residues: 1349 helix: 1.04 (0.21), residues: 628 sheet: 0.41 (0.39), residues: 191 loop : -0.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1171 HIS 0.003 0.001 HIS A 359 PHE 0.019 0.001 PHE A 666 TYR 0.015 0.001 TYR A 405 ARG 0.006 0.000 ARG A 628 *********************** 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 137 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7499 (pptt) REVERT: A 110 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.5974 (tmm) REVERT: A 248 GLN cc_start: 0.8003 (pt0) cc_final: 0.7603 (pt0) REVERT: A 289 ASP cc_start: 0.7277 (m-30) cc_final: 0.7055 (m-30) REVERT: A 479 HIS cc_start: 0.7197 (m90) cc_final: 0.6662 (m90) REVERT: A 608 ARG cc_start: 0.7706 (ttt90) cc_final: 0.7152 (ttm-80) REVERT: A 641 ASP cc_start: 0.8130 (m-30) cc_final: 0.7791 (m-30) REVERT: A 845 LYS cc_start: 0.7743 (mppt) cc_final: 0.7419 (mppt) REVERT: A 851 LYS cc_start: 0.7386 (tptt) cc_final: 0.7000 (tptp) REVERT: A 1179 GLN cc_start: 0.5894 (OUTLIER) cc_final: 0.4999 (mm110) REVERT: B 155 LYS cc_start: 0.6704 (mmpt) cc_final: 0.6328 (tmmm) REVERT: B 188 ILE cc_start: 0.7077 (mm) cc_final: 0.6866 (mt) REVERT: B 215 ARG cc_start: 0.7509 (mtm110) cc_final: 0.7101 (mtm110) REVERT: B 244 ASP cc_start: 0.7910 (t0) cc_final: 0.7592 (m-30) REVERT: B 250 ASN cc_start: 0.7775 (OUTLIER) cc_final: 0.7472 (p0) outliers start: 22 outliers final: 13 residues processed: 127 average time/residue: 1.0790 time to fit residues: 150.7759 Evaluate side-chains 123 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE 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 250 ASN Chi-restraints excluded: chain B residue 295 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11383 Z= 0.231 Angle : 0.582 12.566 15417 Z= 0.291 Chirality : 0.043 0.257 1726 Planarity : 0.005 0.057 1938 Dihedral : 6.677 74.710 1632 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.92 % Allowed : 17.88 % Favored : 80.20 % 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: 0.32 (0.23), residues: 1349 helix: 1.07 (0.21), residues: 630 sheet: 0.34 (0.39), residues: 191 loop : -0.83 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1171 HIS 0.003 0.001 HIS B 283 PHE 0.019 0.001 PHE A 666 TYR 0.014 0.001 TYR A 405 ARG 0.006 0.000 ARG A 628 *********************** 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 133 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.6013 (tmm) REVERT: A 289 ASP cc_start: 0.7299 (m-30) cc_final: 0.7073 (m-30) REVERT: A 479 HIS cc_start: 0.7207 (m90) cc_final: 0.6666 (m90) REVERT: A 608 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7305 (ttm-80) REVERT: A 641 ASP cc_start: 0.8130 (m-30) cc_final: 0.7769 (m-30) REVERT: A 845 LYS cc_start: 0.7764 (mppt) cc_final: 0.7429 (mppt) REVERT: A 851 LYS cc_start: 0.7461 (tptt) cc_final: 0.7064 (tptp) REVERT: A 898 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 1179 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.5022 (mm110) REVERT: B 188 ILE cc_start: 0.7003 (mm) cc_final: 0.6797 (mt) REVERT: B 215 ARG cc_start: 0.7520 (mtm110) cc_final: 0.7107 (mtm110) REVERT: B 244 ASP cc_start: 0.7964 (t0) cc_final: 0.7681 (m-30) REVERT: B 250 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7463 (p0) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 1.0043 time to fit residues: 137.2201 Evaluate side-chains 125 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 255 THR Chi-restraints excluded: chain A residue 333 ILE 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 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 113 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 109 optimal weight: 0.0270 chunk 114 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 0.0980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11383 Z= 0.171 Angle : 0.569 13.401 15417 Z= 0.284 Chirality : 0.042 0.258 1726 Planarity : 0.004 0.056 1938 Dihedral : 6.456 74.470 1632 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.75 % Allowed : 18.46 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.24), residues: 1349 helix: 1.25 (0.22), residues: 626 sheet: 0.47 (0.39), residues: 192 loop : -0.78 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.035 0.001 PHE A 666 TYR 0.013 0.001 TYR A 405 ARG 0.007 0.000 ARG A 628 *********************** 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 134 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5943 (tmm) REVERT: A 241 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6693 (tpt) REVERT: A 289 ASP cc_start: 0.7234 (m-30) cc_final: 0.6984 (m-30) REVERT: A 479 HIS cc_start: 0.7276 (m90) cc_final: 0.6686 (m90) REVERT: A 608 ARG cc_start: 0.7614 (ttt90) cc_final: 0.7187 (ttm-80) REVERT: A 641 ASP cc_start: 0.8103 (m-30) cc_final: 0.7755 (m-30) REVERT: A 845 LYS cc_start: 0.7759 (mppt) cc_final: 0.7427 (mppt) REVERT: A 851 LYS cc_start: 0.7412 (tptt) cc_final: 0.7013 (tptp) REVERT: B 215 ARG cc_start: 0.7526 (mtm110) cc_final: 0.7113 (mtm110) REVERT: B 244 ASP cc_start: 0.7939 (t0) cc_final: 0.7662 (m-30) REVERT: B 250 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7427 (p0) outliers start: 21 outliers final: 11 residues processed: 123 average time/residue: 1.0240 time to fit residues: 139.4977 Evaluate side-chains 120 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU 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 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 128 optimal weight: 0.7980 chunk 78 optimal weight: 0.0970 chunk 60 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 85 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11383 Z= 0.171 Angle : 0.575 13.709 15417 Z= 0.284 Chirality : 0.042 0.260 1726 Planarity : 0.004 0.058 1938 Dihedral : 6.317 74.350 1632 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.25 % Allowed : 19.13 % 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: 0.60 (0.24), residues: 1349 helix: 1.36 (0.22), residues: 627 sheet: 0.51 (0.39), residues: 192 loop : -0.77 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.028 0.001 PHE A 666 TYR 0.013 0.001 TYR A 100 ARG 0.006 0.000 ARG A 628 ********************** 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 130 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5884 (tmm) REVERT: A 241 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6663 (tpt) REVERT: A 289 ASP cc_start: 0.7185 (m-30) cc_final: 0.6937 (m-30) REVERT: A 479 HIS cc_start: 0.7272 (m90) cc_final: 0.6677 (m90) REVERT: A 567 PHE cc_start: 0.6535 (m-80) cc_final: 0.6321 (m-80) REVERT: A 608 ARG cc_start: 0.7674 (ttt90) cc_final: 0.7271 (ttm-80) REVERT: A 641 ASP cc_start: 0.8078 (m-30) cc_final: 0.7733 (m-30) REVERT: A 734 ASP cc_start: 0.7911 (m-30) cc_final: 0.7669 (m-30) REVERT: A 845 LYS cc_start: 0.7758 (mppt) cc_final: 0.7429 (mppt) REVERT: A 851 LYS cc_start: 0.7407 (tptt) cc_final: 0.7015 (tptp) REVERT: B 215 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7118 (mtm110) REVERT: B 244 ASP cc_start: 0.7962 (t0) cc_final: 0.7735 (m-30) REVERT: B 250 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7420 (p0) outliers start: 15 outliers final: 11 residues processed: 123 average time/residue: 1.1490 time to fit residues: 156.0584 Evaluate side-chains 121 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 241 MET Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1038 LEU 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 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 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4154 r_free = 0.4154 target = 0.176093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127985 restraints weight = 12414.386| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.27 r_work: 0.3470 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11383 Z= 0.166 Angle : 0.589 12.953 15417 Z= 0.291 Chirality : 0.041 0.260 1726 Planarity : 0.004 0.058 1938 Dihedral : 6.242 73.990 1632 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.34 % Allowed : 19.38 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1349 helix: 1.39 (0.22), residues: 627 sheet: 0.50 (0.39), residues: 194 loop : -0.73 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1171 HIS 0.004 0.001 HIS A 359 PHE 0.025 0.001 PHE A 666 TYR 0.012 0.001 TYR A 100 ARG 0.006 0.000 ARG A 628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.64 seconds wall clock time: 67 minutes 25.50 seconds (4045.50 seconds total)