Starting phenix.real_space_refine on Wed Mar 4 22:12:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mr2_23954/03_2026/7mr2_23954.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mr2_23954/03_2026/7mr2_23954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mr2_23954/03_2026/7mr2_23954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mr2_23954/03_2026/7mr2_23954.map" model { file = "/net/cci-nas-00/data/ceres_data/7mr2_23954/03_2026/7mr2_23954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mr2_23954/03_2026/7mr2_23954.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10553 2.51 5 N 2927 2.21 5 O 3111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16671 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 6827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 855, 6827 Classifications: {'peptide': 855} Link IDs: {'PTRANS': 34, 'TRANS': 820} Chain breaks: 1 Chain: "C" Number of atoms: 8887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8887 Classifications: {'peptide': 1097} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1032} Chain breaks: 1 Chain: "D" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Time building chain proxies: 3.49, per 1000 atoms: 0.21 Number of scatterers: 16671 At special positions: 0 Unit cell: (141.25, 128.82, 142.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3111 8.00 N 2927 7.00 C 10553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 751.7 milliseconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 13 sheets defined 55.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.813A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 67 through 90 removed outlier: 3.677A pdb=" N GLU B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.886A pdb=" N ARG B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 removed outlier: 3.798A pdb=" N GLU B 123 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.507A pdb=" N ASN B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.110A pdb=" N LEU B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.221A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 198 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 217 through 235 removed outlier: 3.972A pdb=" N THR B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.917A pdb=" N ALA B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.654A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.931A pdb=" N LEU B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 287 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 4.642A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.329A pdb=" N THR B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 334 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 345 " --> pdb=" O ARG B 341 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.549A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.528A pdb=" N ALA B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 420 through 424 removed outlier: 4.041A pdb=" N GLY B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 435 removed outlier: 3.813A pdb=" N MET B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.586A pdb=" N PHE B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 534 removed outlier: 3.650A pdb=" N MET B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 573 removed outlier: 3.747A pdb=" N VAL B 567 " --> pdb=" O GLU B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.084A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.579A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 removed outlier: 3.532A pdb=" N ASN B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 656 removed outlier: 3.567A pdb=" N VAL B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 645 " --> pdb=" O VAL B 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 650 " --> pdb=" O ASP B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 669 removed outlier: 3.511A pdb=" N LEU B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 665 " --> pdb=" O LEU B 661 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 669 " --> pdb=" O MET B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.691A pdb=" N ASP B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 687 " --> pdb=" O ARG B 683 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 688 " --> pdb=" O LEU B 684 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 695 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 716 removed outlier: 3.568A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 712 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 716 " --> pdb=" O SER B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.705A pdb=" N GLN B 725 " --> pdb=" O ALA B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 806 Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 844 removed outlier: 3.950A pdb=" N ARG B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 842 " --> pdb=" O LEU B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 4.116A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.199A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.748A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.148A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.117A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.533A pdb=" N LEU C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.545A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.652A pdb=" N LEU C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.800A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.971A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 633 through 646 removed outlier: 4.278A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.655A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 757 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.143A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 4.047A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 889 removed outlier: 3.704A pdb=" N ALA C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 904 Processing helix chain 'C' and resid 911 through 933 removed outlier: 4.257A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.780A pdb=" N LEU C 980 " --> pdb=" O GLN C 976 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1003 No H-bonds generated for 'chain 'C' and resid 1001 through 1003' Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.545A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1049 removed outlier: 4.093A pdb=" N THR C1048 " --> pdb=" O ALA C1044 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1062 through 1076 removed outlier: 3.982A pdb=" N LYS C1066 " --> pdb=" O SER C1062 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 4.032A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP C1094 " --> pdb=" O TYR C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1114 through 1120 removed outlier: 3.731A pdb=" N ARG C1118 " --> pdb=" O LEU C1114 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 54 through 62 removed outlier: 3.652A pdb=" N LEU D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 87 Processing helix chain 'D' and resid 110 through 124 Processing sheet with id=AA1, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.516A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR B 441 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.526A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 209 removed outlier: 6.188A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR B 768 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 489 removed outlier: 3.583A pdb=" N MET B 541 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.058A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N CYS B 813 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 752 " --> pdb=" O CYS B 813 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.688A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 264 through 265 Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 7.199A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 4.011A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 662 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS C 673 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 675 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 730 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 729 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 731 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 831 through 833 removed outlier: 6.198A pdb=" N VAL C 832 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N TRP C 955 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 965 through 967 removed outlier: 6.787A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 998 " --> pdb=" O TRP C1006 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.877A pdb=" N ASP C1051 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.809A pdb=" N LEU D 102 " --> pdb=" O SER D 92 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5573 1.34 - 1.46: 3311 1.46 - 1.58: 8023 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 17039 Sorted by residual: bond pdb=" CA ASN D 80 " pdb=" CB ASN D 80 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.37e-02 5.33e+03 2.85e+00 bond pdb=" CG1 ILE B 865 " pdb=" CD1 ILE B 865 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CB LYS B 268 " pdb=" CG LYS B 268 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C SER C 419 " pdb=" N PRO C 420 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.62e+00 bond pdb=" CA ASN D 80 " pdb=" C ASN D 80 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.35e-02 5.49e+03 1.48e+00 ... (remaining 17034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 22742 2.40 - 4.80: 305 4.80 - 7.21: 57 7.21 - 9.61: 12 9.61 - 12.01: 7 Bond angle restraints: 23123 Sorted by residual: angle pdb=" C ASN D 80 " pdb=" CA ASN D 80 " pdb=" CB ASN D 80 " ideal model delta sigma weight residual 111.41 119.87 -8.46 1.65e+00 3.67e-01 2.63e+01 angle pdb=" C PHE C 483 " pdb=" N ASP C 484 " pdb=" CA ASP C 484 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.08e+01 angle pdb=" CB MET B 499 " pdb=" CG MET B 499 " pdb=" SD MET B 499 " ideal model delta sigma weight residual 112.70 124.71 -12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB LYS B 268 " pdb=" CG LYS B 268 " pdb=" CD LYS B 268 " ideal model delta sigma weight residual 111.30 120.22 -8.92 2.30e+00 1.89e-01 1.50e+01 angle pdb=" N MET C 569 " pdb=" CA MET C 569 " pdb=" CB MET C 569 " ideal model delta sigma weight residual 110.28 115.90 -5.62 1.55e+00 4.16e-01 1.32e+01 ... (remaining 23118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 9139 17.44 - 34.89: 965 34.89 - 52.33: 152 52.33 - 69.78: 40 69.78 - 87.22: 26 Dihedral angle restraints: 10322 sinusoidal: 4262 harmonic: 6060 Sorted by residual: dihedral pdb=" CA LEU C 460 " pdb=" C LEU C 460 " pdb=" N PRO C 461 " pdb=" CA PRO C 461 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA SER C 268 " pdb=" C SER C 268 " pdb=" N PHE C 269 " pdb=" CA PHE C 269 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ASP B 862 " pdb=" C ASP B 862 " pdb=" N ASP B 863 " pdb=" CA ASP B 863 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 10319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2237 0.073 - 0.146: 284 0.146 - 0.218: 11 0.218 - 0.291: 1 0.291 - 0.364: 1 Chirality restraints: 2534 Sorted by residual: chirality pdb=" CB ILE B 865 " pdb=" CA ILE B 865 " pdb=" CG1 ILE B 865 " pdb=" CG2 ILE B 865 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB THR C 402 " pdb=" CA THR C 402 " pdb=" OG1 THR C 402 " pdb=" CG2 THR C 402 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASP C 484 " pdb=" N ASP C 484 " pdb=" C ASP C 484 " pdb=" CB ASP C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2531 not shown) Planarity restraints: 3042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C1114 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO C1115 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C1115 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C1115 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 582 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO C 583 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 583 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 583 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO C 658 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " -0.041 5.00e-02 4.00e+02 ... (remaining 3039 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3687 2.79 - 3.31: 15624 3.31 - 3.84: 27053 3.84 - 4.37: 29040 4.37 - 4.90: 49456 Nonbonded interactions: 124860 Sorted by model distance: nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.257 3.040 nonbonded pdb=" OH TYR B 200 " pdb=" OE1 GLN B 765 " model vdw 2.290 3.040 nonbonded pdb=" O VAL B 804 " pdb=" NH2 ARG B 808 " model vdw 2.310 3.120 nonbonded pdb=" O SER B 720 " pdb=" OG SER B 720 " model vdw 2.318 3.040 nonbonded pdb=" OE2 GLU C 357 " pdb=" ND2 ASN C 363 " model vdw 2.322 3.120 ... (remaining 124855 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 0.061 17039 Z= 0.151 Angle : 0.752 12.011 23123 Z= 0.381 Chirality : 0.046 0.364 2534 Planarity : 0.006 0.083 3042 Dihedral : 14.956 87.219 6382 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2065 helix: -0.12 (0.15), residues: 1037 sheet: -1.37 (0.42), residues: 161 loop : -1.63 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 186 TYR 0.010 0.001 TYR B 394 PHE 0.030 0.002 PHE D 23 TRP 0.029 0.002 TRP C 544 HIS 0.003 0.001 HIS B 705 Details of bonding type rmsd covalent geometry : bond 0.00313 (17039) covalent geometry : angle 0.75237 (23123) hydrogen bonds : bond 0.12850 ( 735) hydrogen bonds : angle 5.40698 ( 2163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: B 620 MET cc_start: 0.8736 (tpp) cc_final: 0.8493 (tpp) REVERT: C 537 MET cc_start: 0.8330 (ppp) cc_final: 0.8009 (ppp) REVERT: C 1080 MET cc_start: 0.8847 (ppp) cc_final: 0.8542 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1043 time to fit residues: 15.2373 Evaluate side-chains 72 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN B 234 GLN ** C 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 920 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.049376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038671 restraints weight = 128635.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039669 restraints weight = 78274.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040353 restraints weight = 55626.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.040841 restraints weight = 43892.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.041154 restraints weight = 37233.144| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17039 Z= 0.140 Angle : 0.538 7.749 23123 Z= 0.280 Chirality : 0.040 0.157 2534 Planarity : 0.005 0.073 3042 Dihedral : 4.506 21.433 2280 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2065 helix: 0.61 (0.16), residues: 1047 sheet: -1.63 (0.40), residues: 159 loop : -1.45 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 186 TYR 0.012 0.001 TYR B 394 PHE 0.018 0.001 PHE C 789 TRP 0.012 0.001 TRP B 811 HIS 0.003 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00303 (17039) covalent geometry : angle 0.53778 (23123) hydrogen bonds : bond 0.04023 ( 735) hydrogen bonds : angle 4.51614 ( 2163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9229 (ttm) cc_final: 0.8954 (ttp) REVERT: B 620 MET cc_start: 0.9008 (tpp) cc_final: 0.8753 (tpp) REVERT: C 537 MET cc_start: 0.8149 (ppp) cc_final: 0.7714 (ppp) REVERT: C 1080 MET cc_start: 0.8930 (ppp) cc_final: 0.8517 (ppp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1029 time to fit residues: 14.4866 Evaluate side-chains 70 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 28 optimal weight: 0.4980 chunk 102 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 278 ASN ** B 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS C 293 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.037300 restraints weight = 132759.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.038273 restraints weight = 80802.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038944 restraints weight = 57612.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039409 restraints weight = 45680.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.039702 restraints weight = 38816.306| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17039 Z= 0.227 Angle : 0.638 8.023 23123 Z= 0.327 Chirality : 0.042 0.145 2534 Planarity : 0.005 0.084 3042 Dihedral : 4.727 23.837 2280 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 2065 helix: 0.69 (0.16), residues: 1034 sheet: -1.63 (0.40), residues: 153 loop : -1.34 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 808 TYR 0.017 0.002 TYR B 394 PHE 0.012 0.002 PHE C 789 TRP 0.026 0.002 TRP C 587 HIS 0.004 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00490 (17039) covalent geometry : angle 0.63808 (23123) hydrogen bonds : bond 0.04546 ( 735) hydrogen bonds : angle 4.68872 ( 2163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.619 Fit side-chains REVERT: B 518 MET cc_start: 0.8382 (mtp) cc_final: 0.7871 (mtp) REVERT: B 620 MET cc_start: 0.9246 (tpp) cc_final: 0.8992 (tpp) REVERT: C 537 MET cc_start: 0.8223 (ppp) cc_final: 0.7713 (ppp) REVERT: C 1080 MET cc_start: 0.8943 (ppp) cc_final: 0.8566 (ppp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1064 time to fit residues: 14.6892 Evaluate side-chains 66 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 17 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 105 optimal weight: 0.0970 chunk 72 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 673 ASN B 714 HIS B 737 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.048057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.037470 restraints weight = 131544.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.038433 restraints weight = 80342.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039102 restraints weight = 57397.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.039540 restraints weight = 45360.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039879 restraints weight = 38709.314| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17039 Z= 0.209 Angle : 0.615 7.072 23123 Z= 0.314 Chirality : 0.042 0.153 2534 Planarity : 0.005 0.087 3042 Dihedral : 4.714 22.436 2280 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 2065 helix: 0.68 (0.16), residues: 1035 sheet: -1.74 (0.39), residues: 153 loop : -1.34 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 434 TYR 0.016 0.002 TYR B 394 PHE 0.012 0.001 PHE C 599 TRP 0.018 0.001 TRP B 811 HIS 0.004 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00453 (17039) covalent geometry : angle 0.61546 (23123) hydrogen bonds : bond 0.04341 ( 735) hydrogen bonds : angle 4.67727 ( 2163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 620 MET cc_start: 0.9284 (tpp) cc_final: 0.9050 (tpp) REVERT: B 660 MET cc_start: 0.6096 (mpp) cc_final: 0.5853 (mpp) REVERT: C 537 MET cc_start: 0.8214 (ppp) cc_final: 0.7668 (ppp) REVERT: C 1080 MET cc_start: 0.8930 (ppp) cc_final: 0.8580 (ppp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1026 time to fit residues: 14.7351 Evaluate side-chains 68 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 0.0470 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 673 ASN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.048446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.037939 restraints weight = 130242.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038909 restraints weight = 78431.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039550 restraints weight = 55996.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.040030 restraints weight = 44351.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040326 restraints weight = 37679.867| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17039 Z= 0.167 Angle : 0.579 7.791 23123 Z= 0.295 Chirality : 0.041 0.152 2534 Planarity : 0.004 0.082 3042 Dihedral : 4.579 22.336 2280 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 2065 helix: 0.86 (0.16), residues: 1033 sheet: -1.70 (0.39), residues: 153 loop : -1.27 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 9 TYR 0.014 0.001 TYR B 394 PHE 0.028 0.001 PHE C 135 TRP 0.015 0.001 TRP C 504 HIS 0.004 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00366 (17039) covalent geometry : angle 0.57890 (23123) hydrogen bonds : bond 0.04149 ( 735) hydrogen bonds : angle 4.54162 ( 2163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 620 MET cc_start: 0.9280 (tpp) cc_final: 0.9079 (tpp) REVERT: C 287 PHE cc_start: 0.8197 (t80) cc_final: 0.7973 (t80) REVERT: C 667 MET cc_start: 0.6584 (mtt) cc_final: 0.6308 (mtt) REVERT: C 1080 MET cc_start: 0.8945 (ppp) cc_final: 0.8569 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1069 time to fit residues: 15.7451 Evaluate side-chains 69 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 79 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 ASN B 714 HIS C 233 HIS ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.037478 restraints weight = 130860.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038457 restraints weight = 79680.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039101 restraints weight = 56941.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.039576 restraints weight = 45280.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.039899 restraints weight = 38525.962| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17039 Z= 0.192 Angle : 0.610 8.193 23123 Z= 0.309 Chirality : 0.042 0.153 2534 Planarity : 0.004 0.079 3042 Dihedral : 4.641 22.228 2280 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.19), residues: 2065 helix: 0.80 (0.16), residues: 1042 sheet: -1.65 (0.39), residues: 151 loop : -1.31 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 530 TYR 0.022 0.001 TYR C 310 PHE 0.014 0.001 PHE C 135 TRP 0.019 0.001 TRP C 504 HIS 0.009 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00420 (17039) covalent geometry : angle 0.60974 (23123) hydrogen bonds : bond 0.04254 ( 735) hydrogen bonds : angle 4.56887 ( 2163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9198 (ttm) cc_final: 0.8983 (ttm) REVERT: C 287 PHE cc_start: 0.8263 (t80) cc_final: 0.7952 (t80) REVERT: C 396 MET cc_start: 0.9059 (tmm) cc_final: 0.8767 (tmm) REVERT: C 537 MET cc_start: 0.8262 (ppp) cc_final: 0.7881 (ppp) REVERT: C 594 MET cc_start: 0.9420 (tpp) cc_final: 0.9166 (tpp) REVERT: C 1031 MET cc_start: 0.8750 (tpp) cc_final: 0.8271 (tpp) REVERT: C 1080 MET cc_start: 0.8949 (ppp) cc_final: 0.8595 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1060 time to fit residues: 14.9694 Evaluate side-chains 68 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 100 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 193 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 843 GLN C 297 ASN ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.048716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.038168 restraints weight = 129337.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.039116 restraints weight = 78694.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039850 restraints weight = 56914.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040290 restraints weight = 44564.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.040637 restraints weight = 37882.352| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17039 Z= 0.141 Angle : 0.563 7.808 23123 Z= 0.285 Chirality : 0.041 0.152 2534 Planarity : 0.004 0.081 3042 Dihedral : 4.520 21.845 2280 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 2065 helix: 1.00 (0.16), residues: 1027 sheet: -1.67 (0.39), residues: 153 loop : -1.16 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 808 TYR 0.020 0.001 TYR C 310 PHE 0.015 0.001 PHE C 789 TRP 0.012 0.001 TRP B 710 HIS 0.004 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00314 (17039) covalent geometry : angle 0.56309 (23123) hydrogen bonds : bond 0.03952 ( 735) hydrogen bonds : angle 4.38566 ( 2163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9151 (ttm) cc_final: 0.8935 (ttm) REVERT: B 620 MET cc_start: 0.9263 (tpp) cc_final: 0.9060 (tpp) REVERT: C 287 PHE cc_start: 0.8224 (t80) cc_final: 0.7905 (t80) REVERT: C 396 MET cc_start: 0.9024 (tmm) cc_final: 0.8599 (tmm) REVERT: C 537 MET cc_start: 0.8193 (ppp) cc_final: 0.7797 (ppp) REVERT: C 667 MET cc_start: 0.6594 (mtt) cc_final: 0.6315 (mtt) REVERT: C 1080 MET cc_start: 0.8996 (ppp) cc_final: 0.8628 (ppp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1137 time to fit residues: 16.6732 Evaluate side-chains 71 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 101 optimal weight: 0.0670 chunk 22 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 169 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 ASN B 843 GLN C 681 ASN ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.049699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039179 restraints weight = 128662.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.040214 restraints weight = 77401.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040933 restraints weight = 54858.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.041388 restraints weight = 43013.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.041744 restraints weight = 36448.710| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17039 Z= 0.098 Angle : 0.549 12.534 23123 Z= 0.275 Chirality : 0.040 0.154 2534 Planarity : 0.004 0.078 3042 Dihedral : 4.312 22.032 2280 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 2065 helix: 1.17 (0.16), residues: 1033 sheet: -1.44 (0.41), residues: 153 loop : -1.05 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 900 TYR 0.014 0.001 TYR C 310 PHE 0.016 0.001 PHE D 23 TRP 0.012 0.001 TRP B 447 HIS 0.006 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00213 (17039) covalent geometry : angle 0.54931 (23123) hydrogen bonds : bond 0.03582 ( 735) hydrogen bonds : angle 4.22927 ( 2163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9096 (ttm) cc_final: 0.8867 (ttp) REVERT: B 620 MET cc_start: 0.9196 (tpp) cc_final: 0.8995 (tpp) REVERT: C 287 PHE cc_start: 0.8155 (t80) cc_final: 0.7795 (t80) REVERT: C 396 MET cc_start: 0.8942 (tmm) cc_final: 0.8589 (tmm) REVERT: C 537 MET cc_start: 0.8190 (ppp) cc_final: 0.7805 (ppp) REVERT: C 667 MET cc_start: 0.6553 (mtt) cc_final: 0.6235 (mtt) REVERT: C 941 MET cc_start: 0.8818 (tmm) cc_final: 0.8284 (tmm) REVERT: C 1080 MET cc_start: 0.9008 (ppp) cc_final: 0.8666 (ppp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0997 time to fit residues: 14.8260 Evaluate side-chains 73 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 140 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.048618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038131 restraints weight = 129762.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.039117 restraints weight = 78796.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039802 restraints weight = 56249.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040262 restraints weight = 44303.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.040557 restraints weight = 37637.459| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17039 Z= 0.175 Angle : 0.594 12.019 23123 Z= 0.299 Chirality : 0.041 0.229 2534 Planarity : 0.004 0.079 3042 Dihedral : 4.407 21.597 2280 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.19), residues: 2065 helix: 1.13 (0.16), residues: 1026 sheet: -1.53 (0.41), residues: 152 loop : -1.10 (0.22), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 900 TYR 0.019 0.001 TYR C 310 PHE 0.015 0.001 PHE C 789 TRP 0.029 0.001 TRP B 811 HIS 0.006 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00388 (17039) covalent geometry : angle 0.59418 (23123) hydrogen bonds : bond 0.03964 ( 735) hydrogen bonds : angle 4.39312 ( 2163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9140 (ttm) cc_final: 0.8933 (ttm) REVERT: B 620 MET cc_start: 0.9301 (tpp) cc_final: 0.9061 (tpp) REVERT: C 287 PHE cc_start: 0.8257 (t80) cc_final: 0.7867 (t80) REVERT: C 396 MET cc_start: 0.9015 (tmm) cc_final: 0.8753 (tmm) REVERT: C 537 MET cc_start: 0.8190 (ppp) cc_final: 0.7732 (ppp) REVERT: C 594 MET cc_start: 0.9440 (tpp) cc_final: 0.9221 (tpp) REVERT: C 667 MET cc_start: 0.6601 (mtt) cc_final: 0.6279 (mtt) REVERT: C 1080 MET cc_start: 0.9009 (ppp) cc_final: 0.8635 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1017 time to fit residues: 14.4302 Evaluate side-chains 71 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 106 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.049157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.038632 restraints weight = 129322.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.039632 restraints weight = 78036.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040322 restraints weight = 55297.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.040792 restraints weight = 43593.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041117 restraints weight = 37007.908| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17039 Z= 0.126 Angle : 0.564 11.057 23123 Z= 0.282 Chirality : 0.041 0.175 2534 Planarity : 0.004 0.079 3042 Dihedral : 4.335 22.131 2280 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 2065 helix: 1.19 (0.16), residues: 1027 sheet: -1.44 (0.41), residues: 153 loop : -1.07 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 900 TYR 0.016 0.001 TYR C 310 PHE 0.016 0.001 PHE C 789 TRP 0.027 0.001 TRP B 811 HIS 0.006 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00281 (17039) covalent geometry : angle 0.56424 (23123) hydrogen bonds : bond 0.03760 ( 735) hydrogen bonds : angle 4.27664 ( 2163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.9110 (ttm) cc_final: 0.8863 (ttp) REVERT: B 620 MET cc_start: 0.9261 (tpp) cc_final: 0.9021 (tpp) REVERT: C 287 PHE cc_start: 0.8152 (t80) cc_final: 0.7783 (t80) REVERT: C 396 MET cc_start: 0.9009 (tmm) cc_final: 0.8700 (tmm) REVERT: C 537 MET cc_start: 0.8167 (ppp) cc_final: 0.7738 (ppp) REVERT: C 667 MET cc_start: 0.6655 (mtt) cc_final: 0.6314 (mtt) REVERT: C 941 MET cc_start: 0.8849 (tmm) cc_final: 0.8314 (tmm) REVERT: C 1080 MET cc_start: 0.9013 (ppp) cc_final: 0.8657 (ppp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1088 time to fit residues: 15.2365 Evaluate side-chains 69 residues out of total 1784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 17 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037914 restraints weight = 129787.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.038903 restraints weight = 78868.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.039594 restraints weight = 56220.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040054 restraints weight = 44540.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.040358 restraints weight = 37903.088| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17039 Z= 0.167 Angle : 0.598 11.090 23123 Z= 0.300 Chirality : 0.041 0.178 2534 Planarity : 0.004 0.079 3042 Dihedral : 4.432 22.522 2280 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.19), residues: 2065 helix: 1.12 (0.16), residues: 1027 sheet: -1.45 (0.41), residues: 153 loop : -1.08 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 900 TYR 0.018 0.001 TYR C 310 PHE 0.027 0.001 PHE C 901 TRP 0.035 0.001 TRP B 811 HIS 0.006 0.001 HIS B 812 Details of bonding type rmsd covalent geometry : bond 0.00373 (17039) covalent geometry : angle 0.59840 (23123) hydrogen bonds : bond 0.03977 ( 735) hydrogen bonds : angle 4.40175 ( 2163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.82 seconds wall clock time: 37 minutes 41.01 seconds (2261.01 seconds total)