Starting phenix.real_space_refine on Mon Mar 18 11:09:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpx_22991/03_2024/7kpx_22991.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpx_22991/03_2024/7kpx_22991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpx_22991/03_2024/7kpx_22991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpx_22991/03_2024/7kpx_22991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpx_22991/03_2024/7kpx_22991.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpx_22991/03_2024/7kpx_22991.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 77 5.16 5 C 13241 2.51 5 N 3636 2.21 5 O 3808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C GLU 1381": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 898": "NH1" <-> "NH2" Residue "D ARG 1077": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1158": "NH1" <-> "NH2" Residue "D GLU 1163": "OE1" <-> "OE2" Residue "D ARG 1219": "NH1" <-> "NH2" Residue "D ARG 1234": "NH1" <-> "NH2" Residue "D ARG 1238": "NH1" <-> "NH2" Residue "D PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1374": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2952 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2436 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 2 Chain: "C" Number of atoms: 8362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1352, 8362 Classifications: {'peptide': 1352} Incomplete info: {'truncation_to_alanine': 830} Link IDs: {'PTRANS': 41, 'TRANS': 1310} Chain breaks: 3 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 2975 Unresolved non-hydrogen angles: 3799 Unresolved non-hydrogen dihedrals: 2479 Unresolved non-hydrogen chiralities: 290 Planarities with less than four sites: {'GLN:plan1': 43, 'HIS:plan': 17, 'TYR:plan': 32, 'ASN:plan1': 64, 'TRP:plan': 8, 'ASP:plan': 45, 'PHE:plan': 60, 'GLU:plan': 50, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 1540 Chain: "D" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 7012 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 51, 'TRANS': 824} Chain breaks: 2 Time building chain proxies: 10.61, per 1000 atoms: 0.51 Number of scatterers: 20762 At special positions: 0 Unit cell: (123.05, 172.27, 208.65, 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 77 16.00 O 3808 8.00 N 3636 7.00 C 13241 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 3.8 seconds 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5588 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 14 sheets defined 53.2% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.758A pdb=" N ALA A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.898A pdb=" N GLU A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.733A pdb=" N ASN A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.955A pdb=" N ARG A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.702A pdb=" N LEU A 439 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 34 removed outlier: 4.556A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.728A pdb=" N LEU B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.108A pdb=" N VAL B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.032A pdb=" N SER B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.744A pdb=" N ILE B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.236A pdb=" N ILE B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.833A pdb=" N ASP C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.623A pdb=" N HIS C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 166 through 188 Processing helix chain 'C' and resid 198 through 225 removed outlier: 4.105A pdb=" N MET C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.917A pdb=" N ARG C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 272 removed outlier: 3.520A pdb=" N HIS C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.606A pdb=" N HIS C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.674A pdb=" N CYS C 293 " --> pdb=" O TRP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 333 removed outlier: 3.800A pdb=" N THR C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.616A pdb=" N ASN C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.694A pdb=" N SER C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG C 427 " --> pdb=" O ASN C 423 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.524A pdb=" N ILE C 443 " --> pdb=" O PHE C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.587A pdb=" N PHE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 476 removed outlier: 4.112A pdb=" N GLU C 474 " --> pdb=" O ASP C 470 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 476 " --> pdb=" O PRO C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.537A pdb=" N LYS C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE C 495 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 517 Processing helix chain 'C' and resid 524 through 543 removed outlier: 4.218A pdb=" N ASP C 528 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP C 539 " --> pdb=" O GLU C 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 542 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE C 543 " --> pdb=" O TRP C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 572 removed outlier: 3.521A pdb=" N GLN C 552 " --> pdb=" O ASN C 548 " (cutoff:3.500A) Proline residue: C 561 - end of helix removed outlier: 3.547A pdb=" N LEU C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR C 572 " --> pdb=" O ASN C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 Proline residue: C 579 - end of helix removed outlier: 3.782A pdb=" N ILE C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 587 " --> pdb=" O ARG C 583 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.636A pdb=" N SER C 596 " --> pdb=" O TYR C 592 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 removed outlier: 4.648A pdb=" N MET C 615 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS C 616 " --> pdb=" O SER C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 651 removed outlier: 3.951A pdb=" N MET C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 Processing helix chain 'C' and resid 667 through 685 removed outlier: 4.275A pdb=" N LYS C 671 " --> pdb=" O PRO C 667 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 676 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 677 " --> pdb=" O MET C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 704 removed outlier: 3.603A pdb=" N LEU C 695 " --> pdb=" O ASN C 691 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 704 " --> pdb=" O LYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 721 removed outlier: 3.538A pdb=" N HIS C 711 " --> pdb=" O GLU C 707 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 740 removed outlier: 3.637A pdb=" N LEU C 734 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 740 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 removed outlier: 4.064A pdb=" N SER C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 742 through 747' Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 773 through 788 Proline residue: C 782 - end of helix Processing helix chain 'C' and resid 791 through 813 removed outlier: 3.501A pdb=" N LYS C 796 " --> pdb=" O PRO C 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 803 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 804 " --> pdb=" O ASP C 800 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 805 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS C 813 " --> pdb=" O TYR C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 827 removed outlier: 4.024A pdb=" N LYS C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 825 " --> pdb=" O ASN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 854 removed outlier: 4.641A pdb=" N THR C 843 " --> pdb=" O ALA C 839 " (cutoff:3.500A) Proline residue: C 847 - end of helix removed outlier: 3.762A pdb=" N VAL C 852 " --> pdb=" O GLU C 848 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 878 removed outlier: 4.686A pdb=" N ILE C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 893 Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.621A pdb=" N LYS C 906 " --> pdb=" O ASP C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 Processing helix chain 'C' and resid 918 through 927 removed outlier: 3.585A pdb=" N GLN C 923 " --> pdb=" O PHE C 919 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C 927 " --> pdb=" O GLN C 923 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 948 removed outlier: 3.815A pdb=" N ASN C 941 " --> pdb=" O ILE C 937 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 948 " --> pdb=" O GLY C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 963 removed outlier: 3.781A pdb=" N PHE C 962 " --> pdb=" O ILE C 958 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 983 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.502A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Proline residue: C1000 - end of helix Processing helix chain 'C' and resid 1006 through 1023 removed outlier: 3.793A pdb=" N LEU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1072 through 1083 removed outlier: 4.261A pdb=" N GLU C1076 " --> pdb=" O ILE C1072 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1083 " --> pdb=" O VAL C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1103 Processing helix chain 'C' and resid 1106 through 1126 removed outlier: 3.749A pdb=" N GLU C1111 " --> pdb=" O ALA C1107 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C1116 " --> pdb=" O ASP C1112 " (cutoff:3.500A) Processing helix chain 'C' and resid 1128 through 1146 Processing helix chain 'C' and resid 1146 through 1172 removed outlier: 3.998A pdb=" N ASN C1169 " --> pdb=" O LYS C1165 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR C1170 " --> pdb=" O ILE C1166 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C1172 " --> pdb=" O ASP C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1174 through 1196 removed outlier: 3.547A pdb=" N LEU C1181 " --> pdb=" O ILE C1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1218 removed outlier: 3.614A pdb=" N ARG C1208 " --> pdb=" O ILE C1204 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C1218 " --> pdb=" O ASN C1214 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1224 Processing helix chain 'C' and resid 1225 through 1239 removed outlier: 4.166A pdb=" N ILE C1239 " --> pdb=" O HIS C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1251 removed outlier: 4.433A pdb=" N ILE C1243 " --> pdb=" O ILE C1239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C1245 " --> pdb=" O GLN C1241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C1250 " --> pdb=" O ASP C1246 " (cutoff:3.500A) Processing helix chain 'C' and resid 1259 through 1272 Processing helix chain 'C' and resid 1276 through 1296 Processing helix chain 'C' and resid 1307 through 1314 Processing helix chain 'C' and resid 1319 through 1326 removed outlier: 3.673A pdb=" N VAL C1323 " --> pdb=" O VAL C1319 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C1326 " --> pdb=" O PHE C1322 " (cutoff:3.500A) Processing helix chain 'C' and resid 1413 through 1417 Processing helix chain 'D' and resid 33 through 37 removed outlier: 4.050A pdb=" N GLN D 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 33 through 37' Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.971A pdb=" N PHE D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 125 removed outlier: 3.952A pdb=" N LYS D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.681A pdb=" N THR D 220 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.845A pdb=" N ALA D 300 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 822 removed outlier: 3.658A pdb=" N ARG D 822 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 859 removed outlier: 4.133A pdb=" N THR D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 893 Processing helix chain 'D' and resid 900 through 904 removed outlier: 3.955A pdb=" N THR D 904 " --> pdb=" O ASN D 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 900 through 904' Processing helix chain 'D' and resid 958 through 975 removed outlier: 3.649A pdb=" N CYS D 962 " --> pdb=" O PHE D 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER D 964 " --> pdb=" O GLU D 960 " (cutoff:3.500A) Proline residue: D 967 - end of helix Processing helix chain 'D' and resid 1001 through 1019 Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 3.607A pdb=" N ALA D1059 " --> pdb=" O ASN D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1078 Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.679A pdb=" N VAL D1089 " --> pdb=" O GLN D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1188 through 1207 removed outlier: 3.876A pdb=" N ASP D1192 " --> pdb=" O ARG D1188 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP D1199 " --> pdb=" O CYS D1195 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1236 removed outlier: 3.587A pdb=" N LEU D1229 " --> pdb=" O PRO D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1271 removed outlier: 4.055A pdb=" N ASP D1271 " --> pdb=" O PRO D1267 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1364 removed outlier: 3.622A pdb=" N LEU D1350 " --> pdb=" O ASP D1346 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN D1360 " --> pdb=" O GLU D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1365 through 1367 No H-bonds generated for 'chain 'D' and resid 1365 through 1367' Processing helix chain 'D' and resid 1379 through 1392 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 81 removed outlier: 6.803A pdb=" N LYS A 91 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 89 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 88 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 180 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 224 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.596A pdb=" N ILE C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 1373 through 1377 removed outlier: 6.838A pdb=" N ILE C1366 " --> pdb=" O VAL C1375 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C1377 " --> pdb=" O TRP C1364 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP C1364 " --> pdb=" O THR C1377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C1365 " --> pdb=" O ARG D1289 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU D1287 " --> pdb=" O TYR C1367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 153 Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 59 removed outlier: 4.626A pdb=" N LEU D 56 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA8, first strand: chain 'D' and resid 171 through 172 removed outlier: 11.998A pdb=" N HIS D 186 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU D 199 " --> pdb=" O HIS D 186 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 188 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 839 through 842 Processing sheet with id=AB1, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER D1150 " --> pdb=" O CYS D1214 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE D1216 " --> pdb=" O SER D1150 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D1152 " --> pdb=" O ILE D1216 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D1218 " --> pdb=" O ILE D1152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D1154 " --> pdb=" O THR D1218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE D1213 " --> pdb=" O HIS D1241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 915 through 919 Processing sheet with id=AB4, first strand: chain 'D' and resid 950 through 953 removed outlier: 6.659A pdb=" N LYS D 950 " --> pdb=" O LEU D1030 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE D1032 " --> pdb=" O LYS D 950 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 952 " --> pdb=" O ILE D1032 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE D1029 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS D1069 " --> pdb=" O ILE D1029 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE D1031 " --> pdb=" O LYS D1069 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE D1071 " --> pdb=" O ILE D1031 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU D1033 " --> pdb=" O ILE D1071 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 1256 through 1257 1076 hydrogen bonds defined for protein. 3153 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: 7.31 Time building geometry restraints manager: 8.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3707 1.32 - 1.45: 5256 1.45 - 1.57: 12102 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 21185 Sorted by residual: bond pdb=" C LEU C 661 " pdb=" O LEU C 661 " ideal model delta sigma weight residual 1.237 1.296 -0.059 1.17e-02 7.31e+03 2.56e+01 bond pdb=" C ARG C 802 " pdb=" O ARG C 802 " ideal model delta sigma weight residual 1.237 1.293 -0.056 1.17e-02 7.31e+03 2.30e+01 bond pdb=" C GLY C 944 " pdb=" O GLY C 944 " ideal model delta sigma weight residual 1.234 1.290 -0.056 1.20e-02 6.94e+03 2.20e+01 bond pdb=" C VAL C 808 " pdb=" O VAL C 808 " ideal model delta sigma weight residual 1.237 1.288 -0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE C 912 " pdb=" O ILE C 912 " ideal model delta sigma weight residual 1.237 1.283 -0.046 1.17e-02 7.31e+03 1.56e+01 ... (remaining 21180 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.55: 387 105.55 - 113.33: 11774 113.33 - 121.11: 10614 121.11 - 128.88: 5956 128.88 - 136.66: 174 Bond angle restraints: 28905 Sorted by residual: angle pdb=" N LEU C 494 " pdb=" CA LEU C 494 " pdb=" C LEU C 494 " ideal model delta sigma weight residual 111.14 127.60 -16.46 1.08e+00 8.57e-01 2.32e+02 angle pdb=" N ILE C 495 " pdb=" CA ILE C 495 " pdb=" C ILE C 495 " ideal model delta sigma weight residual 113.20 124.91 -11.71 9.60e-01 1.09e+00 1.49e+02 angle pdb=" N PRO D1027 " pdb=" CA PRO D1027 " pdb=" C PRO D1027 " ideal model delta sigma weight residual 110.70 123.97 -13.27 1.22e+00 6.72e-01 1.18e+02 angle pdb=" N ASP C1073 " pdb=" CA ASP C1073 " pdb=" C ASP C1073 " ideal model delta sigma weight residual 111.28 123.07 -11.79 1.09e+00 8.42e-01 1.17e+02 angle pdb=" C PRO D1027 " pdb=" N PRO D1028 " pdb=" CA PRO D1028 " ideal model delta sigma weight residual 119.76 109.94 9.82 1.03e+00 9.43e-01 9.10e+01 ... (remaining 28900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11378 17.94 - 35.88: 903 35.88 - 53.83: 330 53.83 - 71.77: 90 71.77 - 89.71: 13 Dihedral angle restraints: 12714 sinusoidal: 4172 harmonic: 8542 Sorted by residual: dihedral pdb=" CA LEU D 59 " pdb=" C LEU D 59 " pdb=" N LEU D 60 " pdb=" CA LEU D 60 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" N PRO C 613 " pdb=" C PRO C 613 " pdb=" CA PRO C 613 " pdb=" CB PRO C 613 " ideal model delta harmonic sigma weight residual 115.10 129.00 -13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" CA ASP D 12 " pdb=" C ASP D 12 " pdb=" N VAL D 13 " pdb=" CA VAL D 13 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 12711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3171 0.122 - 0.245: 193 0.245 - 0.367: 28 0.367 - 0.490: 7 0.490 - 0.612: 2 Chirality restraints: 3401 Sorted by residual: chirality pdb=" CA LEU C 494 " pdb=" N LEU C 494 " pdb=" C LEU C 494 " pdb=" CB LEU C 494 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.37e+00 chirality pdb=" CA PRO C 613 " pdb=" N PRO C 613 " pdb=" C PRO C 613 " pdb=" CB PRO C 613 " both_signs ideal model delta sigma weight residual False 2.72 2.18 0.54 2.00e-01 2.50e+01 7.21e+00 chirality pdb=" CA PRO C1255 " pdb=" N PRO C1255 " pdb=" C PRO C1255 " pdb=" CB PRO C1255 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 3398 not shown) Planarity restraints: 3735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLU C 340 " 0.070 2.00e-02 2.50e+03 pdb=" O GLU C 340 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN C 341 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C1082 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ASP C1082 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP C1082 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C1083 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 667 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO C 667 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO C 667 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU C 668 " 0.020 2.00e-02 2.50e+03 ... (remaining 3732 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 101 2.50 - 3.10: 14092 3.10 - 3.70: 31653 3.70 - 4.30: 39545 4.30 - 4.90: 66371 Nonbonded interactions: 151762 Sorted by model distance: nonbonded pdb=" O SER C 373 " pdb=" O PHE C1317 " model vdw 1.894 3.040 nonbonded pdb=" O SER C 373 " pdb=" CA GLN C1318 " model vdw 2.132 3.470 nonbonded pdb=" O SER C 373 " pdb=" CB GLN C1318 " model vdw 2.157 3.440 nonbonded pdb=" N ASP B 65 " pdb=" OD1 ASP B 65 " model vdw 2.193 2.520 nonbonded pdb=" O LEU B 66 " pdb=" ND1 HIS B 67 " model vdw 2.270 2.520 ... (remaining 151757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.900 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: 0.020 Extract box with map and model: 12.790 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 54.570 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.006 0.068 21185 Z= 0.399 Angle : 1.066 16.459 28905 Z= 0.739 Chirality : 0.071 0.612 3401 Planarity : 0.007 0.082 3735 Dihedral : 16.336 89.712 7126 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.76 % Favored : 91.89 % Rotamer: Outliers : 17.46 % Allowed : 13.77 % Favored : 68.76 % Cbeta Deviations : 0.18 % 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: -1.80 (0.15), residues: 2847 helix: 0.63 (0.15), residues: 1358 sheet: -2.28 (0.32), residues: 211 loop : -3.17 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 14 HIS 0.010 0.001 HIS A 341 PHE 0.023 0.002 PHE D 294 TYR 0.026 0.002 TYR C 178 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 393 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 VAL cc_start: 0.2279 (OUTLIER) cc_final: 0.2014 (p) REVERT: A 211 CYS cc_start: 0.7930 (t) cc_final: 0.7490 (t) REVERT: A 232 VAL cc_start: 0.7456 (OUTLIER) cc_final: 0.6719 (m) REVERT: A 278 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8534 (m-70) REVERT: A 325 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 347 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8265 (m-30) REVERT: A 350 SER cc_start: 0.9213 (m) cc_final: 0.9008 (p) REVERT: A 446 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5951 (p90) REVERT: B 45 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6895 (t70) REVERT: B 185 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.8899 (ttmt) REVERT: B 212 ILE cc_start: 0.9692 (mt) cc_final: 0.9471 (mt) REVERT: B 233 CYS cc_start: 0.9227 (m) cc_final: 0.8986 (m) REVERT: B 237 THR cc_start: 0.9003 (m) cc_final: 0.8420 (t) REVERT: B 269 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7987 (tp40) REVERT: B 280 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 281 VAL cc_start: 0.9195 (OUTLIER) cc_final: 0.8714 (m) REVERT: C 16 LEU cc_start: 0.8614 (tp) cc_final: 0.8369 (mp) REVERT: C 164 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.5921 (m-80) REVERT: C 203 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: C 218 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7849 (tptp) REVERT: C 337 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5417 (tp) REVERT: C 392 PHE cc_start: 0.7923 (m-80) cc_final: 0.7686 (m-10) REVERT: C 406 MET cc_start: 0.9406 (ttm) cc_final: 0.8494 (tmm) REVERT: C 409 LYS cc_start: 0.9161 (tptt) cc_final: 0.8734 (ttmt) REVERT: C 1425 ASN cc_start: 0.8827 (m-40) cc_final: 0.8198 (m110) REVERT: D 25 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8094 (ptmm) REVERT: D 26 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8561 (tt) REVERT: D 34 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7219 (tptp) REVERT: D 45 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: D 47 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8216 (tpp) REVERT: D 113 LEU cc_start: 0.9343 (tp) cc_final: 0.9119 (tt) REVERT: D 858 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9072 (p) REVERT: D 861 TYR cc_start: 0.7939 (m-80) cc_final: 0.7566 (m-10) REVERT: D 1068 LEU cc_start: 0.8820 (tp) cc_final: 0.8571 (tt) REVERT: D 1083 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9036 (t) REVERT: D 1388 MET cc_start: 0.8510 (mtm) cc_final: 0.8299 (mtt) outliers start: 322 outliers final: 65 residues processed: 645 average time/residue: 0.3123 time to fit residues: 309.9418 Evaluate side-chains 300 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 213 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 30.0000 chunk 115 optimal weight: 5.9990 chunk 224 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 386 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 273 ASN B 291 GLN C 17 HIS C 56 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS D 198 HIS ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 988 ASN D1200 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21185 Z= 0.200 Angle : 0.696 11.496 28905 Z= 0.366 Chirality : 0.047 0.356 3401 Planarity : 0.005 0.069 3735 Dihedral : 5.765 38.520 3030 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.69 % Favored : 92.17 % Rotamer: Outliers : 0.16 % Allowed : 4.18 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: -1.31 (0.16), residues: 2847 helix: 0.95 (0.14), residues: 1416 sheet: -2.18 (0.31), residues: 227 loop : -2.97 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D1332 HIS 0.022 0.001 HIS C 149 PHE 0.030 0.001 PHE D 819 TYR 0.029 0.002 TYR C 387 ARG 0.009 0.001 ARG C 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 283 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ASP cc_start: 0.7918 (p0) cc_final: 0.7636 (p0) REVERT: B 214 ASP cc_start: 0.8065 (t0) cc_final: 0.7788 (t0) REVERT: C 409 LYS cc_start: 0.9050 (tppt) cc_final: 0.8686 (ttmt) REVERT: D 113 LEU cc_start: 0.9428 (tp) cc_final: 0.9207 (tt) REVERT: D 1096 MET cc_start: 0.8801 (mmm) cc_final: 0.8464 (mmm) REVERT: D 1223 ILE cc_start: 0.8812 (tt) cc_final: 0.8306 (pt) REVERT: D 1229 LEU cc_start: 0.9021 (tp) cc_final: 0.8776 (tt) outliers start: 3 outliers final: 2 residues processed: 286 average time/residue: 0.2803 time to fit residues: 130.7485 Evaluate side-chains 181 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 216 optimal weight: 0.0970 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 260 optimal weight: 0.1980 chunk 281 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN D 30 GLN D 198 HIS ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21185 Z= 0.185 Angle : 0.632 13.714 28905 Z= 0.329 Chirality : 0.044 0.268 3401 Planarity : 0.004 0.065 3735 Dihedral : 5.183 32.263 3030 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.48 % Favored : 92.38 % Rotamer: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: -0.81 (0.16), residues: 2847 helix: 1.37 (0.14), residues: 1413 sheet: -1.60 (0.33), residues: 225 loop : -2.80 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D1332 HIS 0.009 0.001 HIS D 29 PHE 0.025 0.001 PHE C 212 TYR 0.027 0.001 TYR C 387 ARG 0.004 0.000 ARG D1158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7115 (tpp) cc_final: 0.6890 (tpp) REVERT: A 211 CYS cc_start: 0.8145 (t) cc_final: 0.7877 (t) REVERT: A 265 SER cc_start: 0.9522 (m) cc_final: 0.9176 (t) REVERT: A 350 SER cc_start: 0.9259 (m) cc_final: 0.8939 (t) REVERT: A 453 ASP cc_start: 0.8000 (p0) cc_final: 0.7749 (p0) REVERT: B 214 ASP cc_start: 0.8171 (t0) cc_final: 0.7956 (t0) REVERT: C 409 LYS cc_start: 0.9100 (tppt) cc_final: 0.8736 (ttmt) REVERT: D 113 LEU cc_start: 0.9464 (tp) cc_final: 0.9241 (tt) REVERT: D 1039 THR cc_start: 0.8419 (p) cc_final: 0.8185 (p) REVERT: D 1096 MET cc_start: 0.8831 (mmm) cc_final: 0.8502 (mmm) REVERT: D 1223 ILE cc_start: 0.8866 (tt) cc_final: 0.8375 (pt) REVERT: D 1352 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7892 (mm-30) outliers start: 2 outliers final: 1 residues processed: 241 average time/residue: 0.2857 time to fit residues: 114.4716 Evaluate side-chains 164 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 136 optimal weight: 20.0000 chunk 247 optimal weight: 0.1980 chunk 74 optimal weight: 7.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 189 GLN B 193 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN C1384 HIS D 148 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 HIS D 976 GLN D1095 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 21185 Z= 0.374 Angle : 0.744 9.766 28905 Z= 0.391 Chirality : 0.046 0.250 3401 Planarity : 0.005 0.061 3735 Dihedral : 5.320 30.942 3030 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.89 % Favored : 90.97 % Rotamer: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: -0.77 (0.16), residues: 2847 helix: 1.45 (0.14), residues: 1412 sheet: -1.49 (0.34), residues: 218 loop : -2.86 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 264 HIS 0.022 0.002 HIS C 109 PHE 0.024 0.002 PHE C 212 TYR 0.026 0.002 TYR C 387 ARG 0.006 0.001 ARG D1158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7635 (tpp) cc_final: 0.7172 (tpp) REVERT: A 211 CYS cc_start: 0.8284 (t) cc_final: 0.8004 (t) REVERT: A 350 SER cc_start: 0.9453 (m) cc_final: 0.9224 (p) REVERT: A 453 ASP cc_start: 0.8337 (p0) cc_final: 0.8029 (p0) REVERT: B 83 MET cc_start: 0.8044 (tpp) cc_final: 0.7761 (tpp) REVERT: B 214 ASP cc_start: 0.8446 (t0) cc_final: 0.8237 (t0) REVERT: B 292 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8234 (tp30) REVERT: D 278 GLN cc_start: 0.7984 (tp40) cc_final: 0.7635 (tp40) REVERT: D 1096 MET cc_start: 0.8928 (mmm) cc_final: 0.8542 (mmm) REVERT: D 1223 ILE cc_start: 0.8853 (tt) cc_final: 0.8453 (pt) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2679 time to fit residues: 87.7244 Evaluate side-chains 133 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 114 optimal weight: 40.0000 chunk 235 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 30.0000 chunk 248 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 397 GLN A 435 HIS B 67 HIS B 186 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1362 GLN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21185 Z= 0.242 Angle : 0.634 9.577 28905 Z= 0.333 Chirality : 0.045 0.274 3401 Planarity : 0.004 0.063 3735 Dihedral : 5.026 28.217 3030 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -0.40 (0.16), residues: 2847 helix: 1.81 (0.14), residues: 1406 sheet: -1.58 (0.33), residues: 226 loop : -2.68 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D1332 HIS 0.006 0.001 HIS C1384 PHE 0.017 0.002 PHE A 355 TYR 0.023 0.002 TYR C 387 ARG 0.005 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 CYS cc_start: 0.8291 (t) cc_final: 0.8033 (t) REVERT: A 262 MET cc_start: 0.9021 (tpp) cc_final: 0.8786 (tpt) REVERT: A 350 SER cc_start: 0.9415 (m) cc_final: 0.9184 (p) REVERT: A 453 ASP cc_start: 0.8441 (p0) cc_final: 0.8241 (p0) REVERT: B 83 MET cc_start: 0.8098 (tpp) cc_final: 0.7726 (tpp) REVERT: D 113 LEU cc_start: 0.9582 (tp) cc_final: 0.9360 (tt) REVERT: D 1068 LEU cc_start: 0.9293 (tp) cc_final: 0.9092 (tp) REVERT: D 1223 ILE cc_start: 0.8888 (tt) cc_final: 0.8416 (pt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2704 time to fit residues: 81.2917 Evaluate side-chains 129 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 276 optimal weight: 2.9990 chunk 229 optimal weight: 0.3980 chunk 128 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 145 optimal weight: 0.0030 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21185 Z= 0.155 Angle : 0.602 10.604 28905 Z= 0.308 Chirality : 0.044 0.313 3401 Planarity : 0.004 0.062 3735 Dihedral : 4.721 26.012 3030 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.90 % Favored : 91.96 % Rotamer: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2847 helix: 2.05 (0.14), residues: 1400 sheet: -1.42 (0.34), residues: 226 loop : -2.53 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D1332 HIS 0.007 0.001 HIS C1384 PHE 0.015 0.001 PHE A 179 TYR 0.016 0.001 TYR B 16 ARG 0.004 0.000 ARG D 941 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.6920 (pmm) cc_final: 0.6599 (mmt) REVERT: A 208 MET cc_start: 0.8740 (ptp) cc_final: 0.8404 (ptp) REVERT: A 211 CYS cc_start: 0.8265 (t) cc_final: 0.8040 (t) REVERT: A 262 MET cc_start: 0.8979 (tpp) cc_final: 0.8727 (tpt) REVERT: D 113 LEU cc_start: 0.9578 (tp) cc_final: 0.9347 (tt) REVERT: D 935 ILE cc_start: 0.9231 (tp) cc_final: 0.8991 (tp) REVERT: D 1096 MET cc_start: 0.9093 (mmm) cc_final: 0.8570 (mmm) REVERT: D 1220 LEU cc_start: 0.9563 (mm) cc_final: 0.9336 (mm) REVERT: D 1223 ILE cc_start: 0.8867 (tt) cc_final: 0.8385 (pt) outliers start: 1 outliers final: 1 residues processed: 186 average time/residue: 0.2685 time to fit residues: 84.8798 Evaluate side-chains 136 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 202 optimal weight: 0.0980 chunk 156 optimal weight: 8.9990 chunk 232 optimal weight: 0.6980 chunk 154 optimal weight: 30.0000 chunk 275 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS B 186 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21185 Z= 0.299 Angle : 0.699 11.279 28905 Z= 0.361 Chirality : 0.045 0.223 3401 Planarity : 0.005 0.091 3735 Dihedral : 4.934 24.556 3030 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.34 % Favored : 90.52 % Rotamer: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.26 (0.17), residues: 2847 helix: 1.91 (0.14), residues: 1421 sheet: -1.57 (0.34), residues: 216 loop : -2.64 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D1332 HIS 0.007 0.001 HIS D 29 PHE 0.025 0.002 PHE B 163 TYR 0.021 0.002 TYR D 118 ARG 0.021 0.001 ARG D 941 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 2.443 Fit side-chains REVERT: A 208 MET cc_start: 0.8775 (ptp) cc_final: 0.8435 (ptp) REVERT: A 211 CYS cc_start: 0.8498 (t) cc_final: 0.8232 (t) REVERT: D 113 LEU cc_start: 0.9604 (tp) cc_final: 0.9370 (tt) REVERT: D 197 MET cc_start: 0.8515 (pmm) cc_final: 0.8298 (pmm) REVERT: D 935 ILE cc_start: 0.9306 (tp) cc_final: 0.9012 (tp) REVERT: D 1068 LEU cc_start: 0.9315 (tp) cc_final: 0.9093 (tp) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.2562 time to fit residues: 72.8069 Evaluate side-chains 125 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 7.9990 chunk 110 optimal weight: 30.0000 chunk 164 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 175 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 216 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1051 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21185 Z= 0.262 Angle : 0.642 10.041 28905 Z= 0.334 Chirality : 0.044 0.207 3401 Planarity : 0.004 0.063 3735 Dihedral : 4.907 23.861 3030 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.47 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.15 (0.17), residues: 2847 helix: 2.07 (0.14), residues: 1402 sheet: -1.72 (0.32), residues: 231 loop : -2.56 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D1332 HIS 0.008 0.001 HIS A 278 PHE 0.019 0.002 PHE A 179 TYR 0.020 0.002 TYR B 68 ARG 0.006 0.001 ARG D 941 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.852 Fit side-chains REVERT: B 44 MET cc_start: 0.4660 (tpt) cc_final: 0.4417 (tpt) REVERT: C 409 LYS cc_start: 0.9240 (tppt) cc_final: 0.8761 (ttmt) REVERT: D 113 LEU cc_start: 0.9576 (tp) cc_final: 0.9347 (tt) REVERT: D 197 MET cc_start: 0.8544 (pmm) cc_final: 0.8322 (pmm) REVERT: D 1068 LEU cc_start: 0.9321 (tp) cc_final: 0.9089 (tp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2750 time to fit residues: 76.3209 Evaluate side-chains 121 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 chunk 154 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 232 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 386 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1408 ASN D 36 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21185 Z= 0.224 Angle : 0.628 10.075 28905 Z= 0.324 Chirality : 0.044 0.193 3401 Planarity : 0.004 0.064 3735 Dihedral : 4.752 23.685 3030 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.92 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.04 (0.17), residues: 2847 helix: 2.20 (0.14), residues: 1405 sheet: -1.84 (0.30), residues: 243 loop : -2.52 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D1332 HIS 0.007 0.001 HIS D 29 PHE 0.018 0.001 PHE A 179 TYR 0.022 0.001 TYR D1284 ARG 0.002 0.000 ARG D1359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 LEU cc_start: 0.7566 (tp) cc_final: 0.7039 (pt) REVERT: C 223 MET cc_start: 0.6845 (tmm) cc_final: 0.6557 (tmm) REVERT: D 113 LEU cc_start: 0.9577 (tp) cc_final: 0.9351 (tt) REVERT: D 935 ILE cc_start: 0.9350 (tp) cc_final: 0.9005 (tp) REVERT: D 1068 LEU cc_start: 0.9369 (tp) cc_final: 0.9166 (tp) REVERT: D 1391 THR cc_start: 0.8033 (p) cc_final: 0.7703 (t) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2837 time to fit residues: 79.0947 Evaluate side-chains 120 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 9.9990 chunk 271 optimal weight: 1.9990 chunk 165 optimal weight: 30.0000 chunk 128 optimal weight: 8.9990 chunk 188 optimal weight: 30.0000 chunk 284 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 226 optimal weight: 0.0970 chunk 23 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN B 207 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN C1408 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1019 ASN D1296 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21185 Z= 0.370 Angle : 0.746 11.250 28905 Z= 0.387 Chirality : 0.046 0.220 3401 Planarity : 0.005 0.057 3735 Dihedral : 5.233 25.451 3030 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.29 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.45 (0.16), residues: 2847 helix: 1.71 (0.14), residues: 1437 sheet: -1.83 (0.32), residues: 229 loop : -2.68 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP D1332 HIS 0.011 0.002 HIS D 295 PHE 0.023 0.002 PHE A 179 TYR 0.027 0.002 TYR C 178 ARG 0.006 0.001 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.6323 (p90) cc_final: 0.6069 (p90) REVERT: A 262 MET cc_start: 0.8881 (tpp) cc_final: 0.8654 (tpt) REVERT: A 458 LEU cc_start: 0.9430 (tp) cc_final: 0.8601 (tp) REVERT: C 223 MET cc_start: 0.7170 (tmm) cc_final: 0.6691 (tmm) REVERT: D 113 LEU cc_start: 0.9608 (tp) cc_final: 0.9396 (tt) REVERT: D 1068 LEU cc_start: 0.9352 (tp) cc_final: 0.9116 (tp) REVERT: D 1391 THR cc_start: 0.8372 (p) cc_final: 0.8046 (t) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2756 time to fit residues: 66.4106 Evaluate side-chains 111 residues out of total 2674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN B 207 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1408 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 GLN ** 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 = 0.3421 r_free = 0.3421 target = 0.067296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.051961 restraints weight = 118759.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053337 restraints weight = 68455.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054266 restraints weight = 46927.191| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21185 Z= 0.171 Angle : 0.616 10.026 28905 Z= 0.317 Chirality : 0.044 0.190 3401 Planarity : 0.004 0.065 3735 Dihedral : 4.740 24.124 3030 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.08 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -0.04 (0.17), residues: 2847 helix: 2.12 (0.14), residues: 1427 sheet: -1.75 (0.31), residues: 241 loop : -2.53 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D1332 HIS 0.008 0.001 HIS C1384 PHE 0.019 0.001 PHE C 179 TYR 0.017 0.001 TYR A 409 ARG 0.003 0.000 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.96 seconds wall clock time: 65 minutes 56.68 seconds (3956.68 seconds total)