Starting phenix.real_space_refine on Sun Aug 24 09:08:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8or3_17116/08_2025/8or3_17116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or3_17116/08_2025/8or3_17116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8or3_17116/08_2025/8or3_17116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or3_17116/08_2025/8or3_17116.map" model { file = "/net/cci-nas-00/data/ceres_data/8or3_17116/08_2025/8or3_17116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or3_17116/08_2025/8or3_17116.cif" } resolution = 2.9 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= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 110 5.16 5 C 11923 2.51 5 N 3177 2.21 5 O 3497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18710 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5720 Classifications: {'peptide': 697} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 685} Chain breaks: 7 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 8894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1143, 8894 Classifications: {'peptide': 1143} Link IDs: {'PTRANS': 54, 'TRANS': 1088} Chain breaks: 5 Chain: "D" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1019 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 941 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 3 Chain: "F" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1402 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 2 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5945 SG CYS B 45 125.953 64.359 41.715 1.00 82.41 S ATOM 6240 SG CYS B 83 124.502 63.438 45.278 1.00 65.16 S ATOM 6169 SG CYS B 75 125.744 77.415 51.920 1.00 61.54 S ATOM 6336 SG CYS B 94 127.660 74.052 51.881 1.00 59.78 S ATOM 6012 SG CYS B 53 121.174 59.988 42.801 1.00 77.07 S ATOM 6035 SG CYS B 56 118.879 59.237 42.742 1.00 85.91 S ATOM 6119 SG CYS B 68 117.194 60.925 42.683 1.00 75.65 S Time building chain proxies: 3.43, per 1000 atoms: 0.18 Number of scatterers: 18710 At special positions: 0 Unit cell: (150.12, 135, 182.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 110 16.00 O 3497 8.00 N 3177 7.00 C 11923 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: 1.11 Conformation dependent library (CDL) restraints added in 680.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B4001 " pdb="ZN ZN B4001 " - pdb=" ND1 HIS B 80 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 45 " pdb="ZN ZN B4001 " - pdb=" SG CYS B 83 " pdb=" ZN B4002 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 75 " pdb="ZN ZN B4002 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B4002 " - pdb=" SG CYS B 94 " pdb=" ZN B4003 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 56 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 53 " pdb="ZN ZN B4003 " - pdb=" SG CYS B 68 " 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 6 sheets defined 71.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 25 through 32 removed outlier: 3.733A pdb=" N TYR A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 54 removed outlier: 4.002A pdb=" N MET A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 4.039A pdb=" N ARG A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 137 removed outlier: 3.528A pdb=" N PHE A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.850A pdb=" N ARG A 142 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 173 through 192 removed outlier: 4.343A pdb=" N LYS A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 removed outlier: 4.183A pdb=" N ILE A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 232 through 255 removed outlier: 3.693A pdb=" N GLN A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 279 removed outlier: 3.632A pdb=" N LYS A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 4.390A pdb=" N ASP A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.654A pdb=" N GLN A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 4.032A pdb=" N ARG A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 355 removed outlier: 3.854A pdb=" N CYS A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.692A pdb=" N TYR A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 405 removed outlier: 3.757A pdb=" N ASN A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 416 through 431 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.615A pdb=" N LYS A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 476 removed outlier: 4.237A pdb=" N PHE A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 496 removed outlier: 3.620A pdb=" N GLU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 525 removed outlier: 3.783A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 504 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.735A pdb=" N TYR A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 565 " --> pdb=" O ARG A 561 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 568 " --> pdb=" O GLN A 564 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 621 through 630 removed outlier: 3.636A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 629 " --> pdb=" O LEU A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 Processing helix chain 'A' and resid 690 through 722 removed outlier: 3.666A pdb=" N GLN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 720 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 removed outlier: 3.813A pdb=" N LEU A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 759 removed outlier: 3.536A pdb=" N ILE A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.241A pdb=" N ASP B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 53 through 59 removed outlier: 3.825A pdb=" N ALA B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.785A pdb=" N GLU B 66 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 19 through 36 removed outlier: 3.755A pdb=" N THR C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.947A pdb=" N GLY C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.638A pdb=" N LEU C 96 " --> pdb=" O CYS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.800A pdb=" N SER C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.568A pdb=" N THR C 185 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 206 removed outlier: 3.704A pdb=" N MET C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 227 removed outlier: 3.589A pdb=" N HIS C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.932A pdb=" N ILE C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 255 removed outlier: 4.268A pdb=" N GLU C 251 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU C 254 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 3.524A pdb=" N PHE C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 270 through 285 removed outlier: 4.008A pdb=" N TYR C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 removed outlier: 4.006A pdb=" N LYS C 303 " --> pdb=" O ASN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 364 removed outlier: 3.621A pdb=" N LEU C 357 " --> pdb=" O ALA C 353 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 360 " --> pdb=" O CYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 374 through 383 removed outlier: 4.619A pdb=" N ALA C 378 " --> pdb=" O THR C 374 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.536A pdb=" N ARG C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 443 Proline residue: C 433 - end of helix Processing helix chain 'C' and resid 447 through 465 removed outlier: 3.518A pdb=" N ARG C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 486 Proline residue: C 478 - end of helix Processing helix chain 'C' and resid 490 through 507 Processing helix chain 'C' and resid 509 through 514 removed outlier: 4.240A pdb=" N PHE C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 514' Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.617A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 Processing helix chain 'C' and resid 561 through 563 No H-bonds generated for 'chain 'C' and resid 561 through 563' Processing helix chain 'C' and resid 564 through 577 removed outlier: 3.543A pdb=" N LEU C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS C 574 " --> pdb=" O THR C 570 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG C 575 " --> pdb=" O CYS C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 Processing helix chain 'C' and resid 606 through 621 removed outlier: 4.422A pdb=" N ASN C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN C 613 " --> pdb=" O PRO C 609 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE C 614 " --> pdb=" O ASN C 610 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 615 " --> pdb=" O THR C 611 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 616 " --> pdb=" O LEU C 612 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 621 " --> pdb=" O GLU C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 644 through 658 removed outlier: 3.804A pdb=" N GLY C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU C 650 " --> pdb=" O PRO C 646 " (cutoff:3.500A) Proline residue: C 653 - end of helix removed outlier: 3.542A pdb=" N PHE C 658 " --> pdb=" O ILE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 681 Processing helix chain 'C' and resid 686 through 695 removed outlier: 3.508A pdb=" N ILE C 690 " --> pdb=" O THR C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 removed outlier: 3.749A pdb=" N LEU C 700 " --> pdb=" O GLU C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 723 Processing helix chain 'C' and resid 724 through 727 removed outlier: 3.558A pdb=" N LEU C 727 " --> pdb=" O PRO C 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.516A pdb=" N ASN C 736 " --> pdb=" O GLY C 732 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 766 removed outlier: 3.592A pdb=" N SER C 753 " --> pdb=" O GLY C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Proline residue: C 782 - end of helix Processing helix chain 'C' and resid 792 through 810 removed outlier: 3.517A pdb=" N TYR C 796 " --> pdb=" O HIS C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 826 removed outlier: 4.016A pdb=" N VAL C 817 " --> pdb=" O GLU C 813 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 818 " --> pdb=" O GLY C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 847 Processing helix chain 'C' and resid 856 through 866 removed outlier: 3.946A pdb=" N VAL C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER C 866 " --> pdb=" O LEU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 869 through 881 removed outlier: 4.102A pdb=" N GLY C 881 " --> pdb=" O SER C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 887 removed outlier: 3.545A pdb=" N VAL C 885 " --> pdb=" O GLY C 881 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY C 886 " --> pdb=" O SER C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 902 removed outlier: 3.559A pdb=" N TYR C 891 " --> pdb=" O ASN C 887 " (cutoff:3.500A) Proline residue: C 893 - end of helix removed outlier: 3.825A pdb=" N THR C 900 " --> pdb=" O LEU C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 920 Processing helix chain 'C' and resid 921 through 926 Processing helix chain 'C' and resid 928 through 939 Processing helix chain 'C' and resid 944 through 961 removed outlier: 3.693A pdb=" N LEU C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 973 removed outlier: 3.651A pdb=" N LEU C 966 " --> pdb=" O ASP C 962 " (cutoff:3.500A) Proline residue: C 968 - end of helix removed outlier: 3.589A pdb=" N TYR C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 991 removed outlier: 3.632A pdb=" N LYS C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 991 " --> pdb=" O THR C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1013 removed outlier: 4.900A pdb=" N GLY C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP C1010 " --> pdb=" O ASN C1006 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE C1011 " --> pdb=" O CYS C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1037 Processing helix chain 'C' and resid 1044 through 1056 Proline residue: C1050 - end of helix Processing helix chain 'C' and resid 1078 through 1096 removed outlier: 3.678A pdb=" N LEU C1093 " --> pdb=" O MET C1089 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C1094 " --> pdb=" O TYR C1090 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER C1095 " --> pdb=" O THR C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1114 removed outlier: 4.135A pdb=" N HIS C1108 " --> pdb=" O GLU C1104 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS C1114 " --> pdb=" O GLU C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1133 removed outlier: 3.887A pdb=" N MET C1121 " --> pdb=" O TYR C1117 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C1122 " --> pdb=" O ASP C1118 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR C1132 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1141 removed outlier: 3.686A pdb=" N VAL C1138 " --> pdb=" O CYS C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1146 through 1153 Processing helix chain 'C' and resid 1162 through 1184 removed outlier: 4.469A pdb=" N GLN C1169 " --> pdb=" O GLU C1165 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP C1170 " --> pdb=" O PHE C1166 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C1172 " --> pdb=" O LYS C1168 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG C1174 " --> pdb=" O ASP C1170 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1210 removed outlier: 4.508A pdb=" N GLU C1207 " --> pdb=" O SER C1203 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C1208 " --> pdb=" O SER C1204 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 103 through 117 removed outlier: 3.842A pdb=" N PHE D 107 " --> pdb=" O GLN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.734A pdb=" N LEU D 122 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'E' and resid 101 through 110 removed outlier: 4.139A pdb=" N LEU E 105 " --> pdb=" O PRO E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 Processing helix chain 'E' and resid 124 through 131 Processing helix chain 'E' and resid 148 through 157 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.655A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 228 Processing helix chain 'F' and resid 65 through 73 removed outlier: 4.386A pdb=" N TYR F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 removed outlier: 3.509A pdb=" N ASP F 91 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 109 removed outlier: 4.290A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 149 removed outlier: 4.233A pdb=" N ILE F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Proline residue: F 142 - end of helix removed outlier: 3.553A pdb=" N LYS F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 165 removed outlier: 3.840A pdb=" N PHE F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN F 163 " --> pdb=" O GLN F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 192 through 199 removed outlier: 3.532A pdb=" N PHE F 199 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 223 removed outlier: 3.740A pdb=" N TRP F 213 " --> pdb=" O PRO F 209 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU F 217 " --> pdb=" O TRP F 213 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASP F 218 " --> pdb=" O ASN F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 541 removed outlier: 6.853A pdb=" N SER A 536 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ALA B 31 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP B 33 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 540 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N TRP B 35 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 30 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 34 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 541 removed outlier: 6.853A pdb=" N SER A 536 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ALA B 31 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN A 538 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N TRP B 33 " --> pdb=" O GLN A 538 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 540 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N TRP B 35 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU A 589 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP B 27 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LYS A 587 " --> pdb=" O TRP B 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 724 through 726 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.878A pdb=" N TRP B 72 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 1063 through 1068 Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.662A pdb=" N VAL D 16 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 6 " --> pdb=" O PHE D 14 " (cutoff:3.500A) 1049 hydrogen bonds defined for protein. 3099 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: 3.01 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3140 1.29 - 1.42: 4514 1.42 - 1.56: 11206 1.56 - 1.69: 2 1.69 - 1.82: 162 Bond restraints: 19024 Sorted by residual: bond pdb=" C ARG B 99 " pdb=" N GLU B 100 " ideal model delta sigma weight residual 1.331 1.508 -0.176 1.33e-02 5.65e+03 1.76e+02 bond pdb=" CA TYR A 620 " pdb=" C TYR A 620 " ideal model delta sigma weight residual 1.522 1.446 0.076 1.23e-02 6.61e+03 3.79e+01 bond pdb=" C TYR A 772 " pdb=" O TYR A 772 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.33e-02 5.65e+03 3.33e+01 bond pdb=" C ASP C 21 " pdb=" O ASP C 21 " ideal model delta sigma weight residual 1.237 1.173 0.063 1.17e-02 7.31e+03 2.93e+01 bond pdb=" CA TYR A 772 " pdb=" C TYR A 772 " ideal model delta sigma weight residual 1.526 1.453 0.074 1.37e-02 5.33e+03 2.88e+01 ... (remaining 19019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 25456 3.16 - 6.32: 190 6.32 - 9.47: 40 9.47 - 12.63: 3 12.63 - 15.79: 3 Bond angle restraints: 25692 Sorted by residual: angle pdb=" N GLU A 654 " pdb=" CA GLU A 654 " pdb=" C GLU A 654 " ideal model delta sigma weight residual 108.02 94.01 14.01 1.75e+00 3.27e-01 6.41e+01 angle pdb=" N ASP A 618 " pdb=" CA ASP A 618 " pdb=" C ASP A 618 " ideal model delta sigma weight residual 110.80 126.59 -15.79 2.13e+00 2.20e-01 5.49e+01 angle pdb=" N VAL A 658 " pdb=" CA VAL A 658 " pdb=" C VAL A 658 " ideal model delta sigma weight residual 111.09 102.61 8.48 1.25e+00 6.40e-01 4.60e+01 angle pdb=" N THR A 616 " pdb=" CA THR A 616 " pdb=" C THR A 616 " ideal model delta sigma weight residual 111.52 120.87 -9.35 1.40e+00 5.10e-01 4.46e+01 angle pdb=" N ASN A 615 " pdb=" CA ASN A 615 " pdb=" C ASN A 615 " ideal model delta sigma weight residual 109.96 100.21 9.75 1.50e+00 4.44e-01 4.22e+01 ... (remaining 25687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10190 18.00 - 36.00: 1170 36.00 - 54.00: 267 54.00 - 72.00: 64 72.00 - 89.99: 16 Dihedral angle restraints: 11707 sinusoidal: 4800 harmonic: 6907 Sorted by residual: dihedral pdb=" N ASP A 618 " pdb=" C ASP A 618 " pdb=" CA ASP A 618 " pdb=" CB ASP A 618 " ideal model delta harmonic sigma weight residual 122.80 140.58 -17.78 0 2.50e+00 1.60e-01 5.06e+01 dihedral pdb=" C ASP A 618 " pdb=" N ASP A 618 " pdb=" CA ASP A 618 " pdb=" CB ASP A 618 " ideal model delta harmonic sigma weight residual -122.60 -138.71 16.11 0 2.50e+00 1.60e-01 4.15e+01 dihedral pdb=" C THR A 616 " pdb=" N THR A 616 " pdb=" CA THR A 616 " pdb=" CB THR A 616 " ideal model delta harmonic sigma weight residual -122.00 -133.43 11.43 0 2.50e+00 1.60e-01 2.09e+01 ... (remaining 11704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 2966 0.172 - 0.343: 17 0.343 - 0.515: 2 0.515 - 0.686: 1 0.686 - 0.858: 1 Chirality restraints: 2987 Sorted by residual: chirality pdb=" CA ASP A 618 " pdb=" N ASP A 618 " pdb=" C ASP A 618 " pdb=" CB ASP A 618 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.84e+01 chirality pdb=" CA THR A 616 " pdb=" N THR A 616 " pdb=" C THR A 616 " pdb=" CB THR A 616 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" CA TYR A 675 " pdb=" N TYR A 675 " pdb=" C TYR A 675 " pdb=" CB TYR A 675 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 ... (remaining 2984 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 612 " -0.031 2.00e-02 2.50e+03 6.19e-02 3.83e+01 pdb=" C LEU A 612 " 0.107 2.00e-02 2.50e+03 pdb=" O LEU A 612 " -0.040 2.00e-02 2.50e+03 pdb=" N GLN A 613 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 764 " -0.440 9.50e-02 1.11e+02 1.97e-01 2.38e+01 pdb=" NE ARG A 764 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 764 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 764 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 764 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 681 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.69e+01 pdb=" C ARG A 681 " 0.071 2.00e-02 2.50e+03 pdb=" O ARG A 681 " -0.027 2.00e-02 2.50e+03 pdb=" N VAL A 682 " -0.023 2.00e-02 2.50e+03 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 149 2.59 - 3.16: 15352 3.16 - 3.74: 28980 3.74 - 4.32: 36524 4.32 - 4.90: 62331 Nonbonded interactions: 143336 Sorted by model distance: nonbonded pdb=" OD2 ASP B 97 " pdb="ZN ZN B4002 " model vdw 2.008 2.230 nonbonded pdb=" OD1 ASN A 615 " pdb=" O LYS B 20 " model vdw 2.189 3.040 nonbonded pdb=" OD1 ASN A 176 " pdb=" OH TYR A 208 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 107 " pdb=" OE1 GLU C 153 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR D 137 " pdb=" OE1 GLU D 140 " model vdw 2.211 3.040 ... (remaining 143331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.005 0.176 19033 Z= 0.321 Angle : 0.716 15.788 25692 Z= 0.402 Chirality : 0.047 0.858 2987 Planarity : 0.006 0.197 3244 Dihedral : 16.269 89.994 7187 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 0.95 % Allowed : 18.37 % Favored : 80.68 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.22 (0.18), residues: 2291 helix: 1.82 (0.14), residues: 1509 sheet: 0.27 (0.96), residues: 34 loop : -1.33 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 23 TYR 0.024 0.001 TYR A 52 PHE 0.034 0.001 PHE C 24 TRP 0.010 0.001 TRP F 213 HIS 0.002 0.000 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00526 (19024) covalent geometry : angle 0.71618 (25692) hydrogen bonds : bond 0.15047 ( 1049) hydrogen bonds : angle 5.43746 ( 3099) metal coordination : bond 0.00272 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 338 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.7086 (pttt) REVERT: A 705 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7630 (mp0) REVERT: C 15 MET cc_start: 0.7733 (ttm) cc_final: 0.7352 (mtt) REVERT: C 20 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7526 (mttm) REVERT: C 266 VAL cc_start: 0.8395 (t) cc_final: 0.8194 (t) REVERT: C 1169 GLN cc_start: 0.7243 (pm20) cc_final: 0.6805 (mp10) REVERT: C 1171 GLU cc_start: 0.6970 (mp0) cc_final: 0.6091 (mp0) outliers start: 20 outliers final: 12 residues processed: 349 average time/residue: 0.5909 time to fit residues: 229.7154 Evaluate side-chains 332 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 319 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 LYS Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 897 GLN Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 174 ASP Chi-restraints excluded: chain F residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 624 GLN A 728 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN D 158 GLN F 183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131364 restraints weight = 27332.275| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.95 r_work: 0.3584 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19033 Z= 0.212 Angle : 0.631 8.776 25692 Z= 0.325 Chirality : 0.043 0.175 2987 Planarity : 0.005 0.070 3244 Dihedral : 5.014 66.334 2521 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.27 % Allowed : 15.96 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2291 helix: 1.71 (0.14), residues: 1535 sheet: -0.54 (0.87), residues: 44 loop : -1.21 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 25 TYR 0.023 0.002 TYR A 157 PHE 0.020 0.002 PHE A 402 TRP 0.010 0.002 TRP B 72 HIS 0.006 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00506 (19024) covalent geometry : angle 0.63064 (25692) hydrogen bonds : bond 0.05989 ( 1049) hydrogen bonds : angle 4.10482 ( 3099) metal coordination : bond 0.00680 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 367 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7518 (tpp80) cc_final: 0.7265 (tpp80) REVERT: A 330 GLN cc_start: 0.6829 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 675 TYR cc_start: 0.7904 (t80) cc_final: 0.7699 (t80) REVERT: A 688 MET cc_start: 0.7658 (mtt) cc_final: 0.7401 (mtt) REVERT: A 735 LEU cc_start: 0.8672 (mt) cc_final: 0.8341 (mp) REVERT: A 754 ASP cc_start: 0.8317 (m-30) cc_final: 0.8036 (m-30) REVERT: A 768 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6190 (tm-30) REVERT: C 46 GLU cc_start: 0.7261 (mp0) cc_final: 0.6640 (mp0) REVERT: C 70 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: C 138 LEU cc_start: 0.8430 (mt) cc_final: 0.8180 (mt) REVERT: C 156 ASP cc_start: 0.8046 (m-30) cc_final: 0.7719 (m-30) REVERT: C 691 ASP cc_start: 0.7699 (p0) cc_final: 0.7426 (p0) REVERT: C 721 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7582 (mttp) REVERT: C 890 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 897 GLN cc_start: 0.7955 (tm130) cc_final: 0.7644 (tm130) REVERT: C 915 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7507 (tm-30) REVERT: C 1044 LEU cc_start: 0.8173 (mt) cc_final: 0.7866 (mp) REVERT: C 1077 ASP cc_start: 0.7577 (t0) cc_final: 0.7239 (t0) REVERT: C 1158 LYS cc_start: 0.8084 (tttt) cc_final: 0.7856 (tttt) REVERT: C 1167 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7065 (tm-30) REVERT: C 1169 GLN cc_start: 0.7444 (pm20) cc_final: 0.7113 (pm20) REVERT: C 1171 GLU cc_start: 0.7470 (mp0) cc_final: 0.6965 (mp0) REVERT: F 181 TYR cc_start: 0.7785 (m-80) cc_final: 0.7165 (m-80) outliers start: 69 outliers final: 23 residues processed: 401 average time/residue: 0.5357 time to fit residues: 241.1549 Evaluate side-chains 379 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 721 LYS Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 86 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 154 optimal weight: 1.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN F 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.127963 restraints weight = 27336.917| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.92 r_work: 0.3541 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19033 Z= 0.211 Angle : 0.621 9.333 25692 Z= 0.320 Chirality : 0.043 0.173 2987 Planarity : 0.005 0.071 3244 Dihedral : 4.484 53.215 2501 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.12 % Allowed : 17.09 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.99 (0.18), residues: 2291 helix: 1.57 (0.14), residues: 1534 sheet: 0.43 (0.92), residues: 34 loop : -1.35 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1024 TYR 0.036 0.002 TYR A 157 PHE 0.020 0.002 PHE A 402 TRP 0.013 0.002 TRP B 72 HIS 0.007 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00511 (19024) covalent geometry : angle 0.62093 (25692) hydrogen bonds : bond 0.06173 ( 1049) hydrogen bonds : angle 4.09865 ( 3099) metal coordination : bond 0.00680 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 389 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.7906 (t80) cc_final: 0.7704 (t80) REVERT: A 108 GLU cc_start: 0.7863 (tp30) cc_final: 0.7635 (tp30) REVERT: A 142 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5014 (pmt-80) REVERT: A 330 GLN cc_start: 0.7012 (tm-30) cc_final: 0.6767 (tm-30) REVERT: A 397 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8409 (mtmt) REVERT: A 469 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7369 (mtt) REVERT: A 578 LYS cc_start: 0.8526 (pptt) cc_final: 0.8139 (pttm) REVERT: A 621 THR cc_start: 0.8395 (m) cc_final: 0.8166 (p) REVERT: A 675 TYR cc_start: 0.8052 (t80) cc_final: 0.7695 (t80) REVERT: A 688 MET cc_start: 0.8186 (mtt) cc_final: 0.7964 (mtt) REVERT: A 735 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8234 (mp) REVERT: A 750 LYS cc_start: 0.8017 (mtpp) cc_final: 0.7606 (mtmm) REVERT: A 754 ASP cc_start: 0.8312 (m-30) cc_final: 0.7908 (m-30) REVERT: B 87 TRP cc_start: 0.8698 (t-100) cc_final: 0.8474 (t-100) REVERT: C 44 ASP cc_start: 0.6488 (t0) cc_final: 0.5941 (t70) REVERT: C 46 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: C 48 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7719 (mtmp) REVERT: C 70 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8501 (mttp) REVERT: C 116 GLU cc_start: 0.7717 (tp30) cc_final: 0.7512 (tp30) REVERT: C 138 LEU cc_start: 0.8362 (mt) cc_final: 0.8090 (mt) REVERT: C 156 ASP cc_start: 0.8034 (m-30) cc_final: 0.7501 (m-30) REVERT: C 194 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8019 (mmm-85) REVERT: C 221 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.6494 (tp30) REVERT: C 280 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6488 (tm-30) REVERT: C 370 GLU cc_start: 0.7267 (tm-30) cc_final: 0.7037 (tp30) REVERT: C 506 CYS cc_start: 0.8354 (t) cc_final: 0.8032 (m) REVERT: C 557 SER cc_start: 0.8577 (t) cc_final: 0.8358 (p) REVERT: C 660 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8285 (mpp80) REVERT: C 691 ASP cc_start: 0.7806 (p0) cc_final: 0.7462 (p0) REVERT: C 703 GLU cc_start: 0.7961 (pp20) cc_final: 0.7735 (pp20) REVERT: C 863 GLU cc_start: 0.8278 (tp30) cc_final: 0.7987 (tm-30) REVERT: C 890 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 897 GLN cc_start: 0.7916 (tm130) cc_final: 0.7574 (tm130) REVERT: C 915 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: C 1016 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: C 1044 LEU cc_start: 0.8081 (mt) cc_final: 0.7802 (mp) REVERT: C 1057 LYS cc_start: 0.8582 (mttm) cc_final: 0.8353 (mttp) REVERT: C 1075 VAL cc_start: 0.8667 (t) cc_final: 0.8309 (m) REVERT: C 1158 LYS cc_start: 0.8157 (tttt) cc_final: 0.7950 (tttt) REVERT: C 1165 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7090 (tp30) REVERT: C 1167 GLU cc_start: 0.7679 (tm-30) cc_final: 0.6820 (tm-30) REVERT: C 1169 GLN cc_start: 0.7462 (pm20) cc_final: 0.6879 (pm20) REVERT: C 1171 GLU cc_start: 0.7436 (mp0) cc_final: 0.6612 (mp0) REVERT: D 7 GLN cc_start: 0.2632 (OUTLIER) cc_final: 0.2080 (mm110) REVERT: F 144 MET cc_start: 0.5276 (pp-130) cc_final: 0.4987 (pp-130) REVERT: F 181 TYR cc_start: 0.7806 (m-80) cc_final: 0.6918 (m-80) outliers start: 87 outliers final: 32 residues processed: 432 average time/residue: 0.5809 time to fit residues: 279.8973 Evaluate side-chains 424 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 380 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 148 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 192 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 361 ASN A 386 ASN A 694 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.156237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129524 restraints weight = 27393.326| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.92 r_work: 0.3558 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19033 Z= 0.152 Angle : 0.561 9.765 25692 Z= 0.290 Chirality : 0.040 0.157 2987 Planarity : 0.005 0.069 3244 Dihedral : 4.079 21.638 2495 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.65 % Allowed : 19.08 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.10 (0.18), residues: 2291 helix: 1.66 (0.14), residues: 1535 sheet: -0.45 (0.85), residues: 44 loop : -1.26 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1024 TYR 0.023 0.001 TYR C 772 PHE 0.018 0.001 PHE A 402 TRP 0.010 0.001 TRP B 33 HIS 0.004 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00355 (19024) covalent geometry : angle 0.56141 (25692) hydrogen bonds : bond 0.05049 ( 1049) hydrogen bonds : angle 3.91803 ( 3099) metal coordination : bond 0.00441 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 377 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.8046 (t80) cc_final: 0.7762 (t80) REVERT: A 330 GLN cc_start: 0.6950 (tm-30) cc_final: 0.6707 (tm-30) REVERT: A 469 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: A 578 LYS cc_start: 0.8506 (pptt) cc_final: 0.8274 (pttp) REVERT: A 589 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 621 THR cc_start: 0.8259 (m) cc_final: 0.8038 (p) REVERT: A 675 TYR cc_start: 0.8079 (t80) cc_final: 0.7790 (t80) REVERT: A 677 ASN cc_start: 0.8059 (t0) cc_final: 0.7729 (t0) REVERT: A 679 LYS cc_start: 0.7649 (mppt) cc_final: 0.7420 (mppt) REVERT: A 735 LEU cc_start: 0.8628 (mt) cc_final: 0.8296 (mp) REVERT: A 750 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7680 (mtmm) REVERT: A 754 ASP cc_start: 0.8251 (m-30) cc_final: 0.7894 (m-30) REVERT: B 87 TRP cc_start: 0.8733 (t-100) cc_final: 0.8513 (t-100) REVERT: C 70 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: C 138 LEU cc_start: 0.8424 (mt) cc_final: 0.8140 (mt) REVERT: C 156 ASP cc_start: 0.8062 (m-30) cc_final: 0.7549 (m-30) REVERT: C 194 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (mmm-85) REVERT: C 221 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.6523 (tp30) REVERT: C 366 GLU cc_start: 0.7960 (mp0) cc_final: 0.7600 (mp0) REVERT: C 382 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7630 (mtt90) REVERT: C 660 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8291 (mpp80) REVERT: C 703 GLU cc_start: 0.7966 (pp20) cc_final: 0.7600 (pp20) REVERT: C 863 GLU cc_start: 0.8280 (tp30) cc_final: 0.7967 (tm-30) REVERT: C 890 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 897 GLN cc_start: 0.7942 (tm130) cc_final: 0.7671 (tm130) REVERT: C 969 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8070 (ttp-170) REVERT: C 1016 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: C 1044 LEU cc_start: 0.8153 (mt) cc_final: 0.7875 (mp) REVERT: C 1057 LYS cc_start: 0.8500 (mttm) cc_final: 0.8290 (mttp) REVERT: C 1075 VAL cc_start: 0.8674 (t) cc_final: 0.8347 (m) REVERT: C 1142 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8445 (tt) REVERT: C 1167 GLU cc_start: 0.7757 (tm-30) cc_final: 0.6887 (tm-30) REVERT: C 1171 GLU cc_start: 0.7378 (mp0) cc_final: 0.6630 (mp0) REVERT: D 7 GLN cc_start: 0.2604 (OUTLIER) cc_final: 0.2146 (mm110) REVERT: F 144 MET cc_start: 0.5307 (pp-130) cc_final: 0.4993 (pp-130) REVERT: F 181 TYR cc_start: 0.7898 (m-80) cc_final: 0.7005 (m-80) outliers start: 77 outliers final: 33 residues processed: 419 average time/residue: 0.5991 time to fit residues: 279.3702 Evaluate side-chains 410 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 368 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 969 ARG Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1114 LYS Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 120 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 597 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128738 restraints weight = 27107.374| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.92 r_work: 0.3561 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19033 Z= 0.143 Angle : 0.565 11.726 25692 Z= 0.288 Chirality : 0.039 0.156 2987 Planarity : 0.005 0.068 3244 Dihedral : 4.014 20.517 2495 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.36 % Allowed : 20.12 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.15 (0.18), residues: 2291 helix: 1.73 (0.14), residues: 1531 sheet: -0.38 (0.84), residues: 44 loop : -1.33 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 25 TYR 0.025 0.001 TYR A 672 PHE 0.016 0.001 PHE A 402 TRP 0.010 0.001 TRP B 33 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00333 (19024) covalent geometry : angle 0.56472 (25692) hydrogen bonds : bond 0.04762 ( 1049) hydrogen bonds : angle 3.84363 ( 3099) metal coordination : bond 0.00387 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 373 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.8027 (t80) cc_final: 0.7707 (t80) REVERT: A 143 HIS cc_start: 0.5819 (OUTLIER) cc_final: 0.5540 (m-70) REVERT: A 330 GLN cc_start: 0.6907 (tm-30) cc_final: 0.6637 (tm-30) REVERT: A 469 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7171 (mtt) REVERT: A 578 LYS cc_start: 0.8572 (pptt) cc_final: 0.8327 (pttp) REVERT: A 589 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7962 (mt-10) REVERT: A 592 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6884 (t) REVERT: A 615 ASN cc_start: 0.8091 (m-40) cc_final: 0.7891 (m-40) REVERT: A 621 THR cc_start: 0.8312 (m) cc_final: 0.8034 (p) REVERT: A 642 ILE cc_start: 0.8536 (mt) cc_final: 0.8302 (tt) REVERT: A 644 LEU cc_start: 0.8245 (mp) cc_final: 0.7970 (mp) REVERT: A 675 TYR cc_start: 0.8059 (t80) cc_final: 0.7772 (t80) REVERT: A 735 LEU cc_start: 0.8575 (mt) cc_final: 0.8240 (mp) REVERT: B 87 TRP cc_start: 0.8679 (t-100) cc_final: 0.8436 (t-100) REVERT: C 46 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 70 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8430 (mttp) REVERT: C 138 LEU cc_start: 0.8346 (mt) cc_final: 0.8048 (mt) REVERT: C 156 ASP cc_start: 0.8044 (m-30) cc_final: 0.7486 (m-30) REVERT: C 194 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8038 (mmm-85) REVERT: C 221 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.6832 (tp30) REVERT: C 226 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.7183 (m-30) REVERT: C 362 SER cc_start: 0.8183 (t) cc_final: 0.7870 (m) REVERT: C 366 GLU cc_start: 0.8010 (mp0) cc_final: 0.7621 (mp0) REVERT: C 382 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7663 (mtt90) REVERT: C 554 ASP cc_start: 0.7957 (p0) cc_final: 0.7633 (p0) REVERT: C 660 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8255 (mpp80) REVERT: C 691 ASP cc_start: 0.7818 (p0) cc_final: 0.7347 (p0) REVERT: C 863 GLU cc_start: 0.8289 (tp30) cc_final: 0.7953 (tm-30) REVERT: C 890 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 897 GLN cc_start: 0.7887 (tm130) cc_final: 0.7601 (tm130) REVERT: C 969 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8014 (ttp-170) REVERT: C 971 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8224 (tmtp) REVERT: C 1044 LEU cc_start: 0.8129 (mt) cc_final: 0.7854 (mp) REVERT: C 1057 LYS cc_start: 0.8514 (mttm) cc_final: 0.8293 (mttp) REVERT: C 1075 VAL cc_start: 0.8636 (t) cc_final: 0.8302 (m) REVERT: C 1142 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 1167 GLU cc_start: 0.7691 (tm-30) cc_final: 0.6764 (tm-30) REVERT: C 1171 GLU cc_start: 0.7440 (mp0) cc_final: 0.6487 (mp0) REVERT: D 7 GLN cc_start: 0.2709 (OUTLIER) cc_final: 0.2177 (mm110) REVERT: F 144 MET cc_start: 0.5221 (pp-130) cc_final: 0.4814 (pp-130) REVERT: F 157 PHE cc_start: 0.6495 (t80) cc_final: 0.6091 (t80) REVERT: F 181 TYR cc_start: 0.7786 (m-80) cc_final: 0.6953 (m-80) outliers start: 71 outliers final: 37 residues processed: 410 average time/residue: 0.6001 time to fit residues: 274.6472 Evaluate side-chains 413 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 607 ASP Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 938 LYS Chi-restraints excluded: chain C residue 969 ARG Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 212 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 194 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 216 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 345 HIS A 361 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN C1169 GLN F 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.155187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128241 restraints weight = 27059.203| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.90 r_work: 0.3543 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19033 Z= 0.170 Angle : 0.586 10.943 25692 Z= 0.299 Chirality : 0.041 0.164 2987 Planarity : 0.005 0.068 3244 Dihedral : 4.074 20.548 2495 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.17 % Allowed : 19.74 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.07 (0.18), residues: 2291 helix: 1.67 (0.14), residues: 1533 sheet: -0.28 (0.84), residues: 44 loop : -1.37 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 25 TYR 0.021 0.002 TYR C 772 PHE 0.016 0.002 PHE A 95 TRP 0.010 0.001 TRP B 33 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00407 (19024) covalent geometry : angle 0.58648 (25692) hydrogen bonds : bond 0.05254 ( 1049) hydrogen bonds : angle 3.91406 ( 3099) metal coordination : bond 0.00522 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 366 time to evaluate : 0.738 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 52 TYR cc_start: 0.8030 (t80) cc_final: 0.7689 (t80) REVERT: A 139 TYR cc_start: 0.8128 (t80) cc_final: 0.7529 (t80) REVERT: A 142 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.4778 (pmt-80) REVERT: A 330 GLN cc_start: 0.6920 (tm-30) cc_final: 0.6633 (tm-30) REVERT: A 469 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7301 (mtt) REVERT: A 578 LYS cc_start: 0.8569 (pptt) cc_final: 0.8149 (pttm) REVERT: A 589 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 592 THR cc_start: 0.7155 (OUTLIER) cc_final: 0.6925 (t) REVERT: A 621 THR cc_start: 0.8330 (m) cc_final: 0.8025 (p) REVERT: A 644 LEU cc_start: 0.8206 (mp) cc_final: 0.7946 (mp) REVERT: A 675 TYR cc_start: 0.8077 (t80) cc_final: 0.7749 (t80) REVERT: A 679 LYS cc_start: 0.7707 (mppt) cc_final: 0.7402 (mppt) REVERT: A 735 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 754 ASP cc_start: 0.8369 (m-30) cc_final: 0.8002 (m-30) REVERT: B 87 TRP cc_start: 0.8695 (t-100) cc_final: 0.8446 (t-100) REVERT: C 46 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7288 (mm-30) REVERT: C 70 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8454 (mttp) REVERT: C 138 LEU cc_start: 0.8346 (mt) cc_final: 0.8047 (mt) REVERT: C 156 ASP cc_start: 0.8034 (m-30) cc_final: 0.7468 (m-30) REVERT: C 194 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8050 (mmm-85) REVERT: C 221 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: C 226 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.7240 (m-30) REVERT: C 272 ARG cc_start: 0.7451 (mtp-110) cc_final: 0.7235 (mtp-110) REVERT: C 358 ASP cc_start: 0.7832 (t0) cc_final: 0.7606 (t0) REVERT: C 362 SER cc_start: 0.8199 (t) cc_final: 0.7878 (m) REVERT: C 366 GLU cc_start: 0.8005 (mp0) cc_final: 0.7611 (mp0) REVERT: C 382 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7774 (mtt90) REVERT: C 554 ASP cc_start: 0.7932 (p0) cc_final: 0.7612 (p0) REVERT: C 660 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8231 (mpp80) REVERT: C 863 GLU cc_start: 0.8351 (tp30) cc_final: 0.7999 (tm-30) REVERT: C 890 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7514 (tm-30) REVERT: C 897 GLN cc_start: 0.7889 (tm130) cc_final: 0.7563 (tm130) REVERT: C 969 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: C 971 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8271 (tmtp) REVERT: C 1057 LYS cc_start: 0.8554 (mttm) cc_final: 0.8332 (mttp) REVERT: C 1075 VAL cc_start: 0.8635 (t) cc_final: 0.8321 (m) REVERT: C 1142 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8365 (tt) REVERT: C 1167 GLU cc_start: 0.7646 (tm-30) cc_final: 0.6305 (tm-30) REVERT: C 1171 GLU cc_start: 0.7373 (mp0) cc_final: 0.6408 (mp0) REVERT: C 1175 SER cc_start: 0.8397 (t) cc_final: 0.7881 (p) REVERT: D 7 GLN cc_start: 0.2683 (OUTLIER) cc_final: 0.2169 (mm110) REVERT: F 144 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4855 (pp-130) REVERT: F 157 PHE cc_start: 0.6527 (t80) cc_final: 0.6099 (t80) REVERT: F 181 TYR cc_start: 0.7754 (m-80) cc_final: 0.6806 (m-80) outliers start: 88 outliers final: 48 residues processed: 413 average time/residue: 0.5704 time to fit residues: 262.4018 Evaluate side-chains 426 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 938 LYS Chi-restraints excluded: chain C residue 969 ARG Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 227 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 99 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 361 ASN A 597 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN C1140 GLN C1169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.155177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128171 restraints weight = 27167.903| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.92 r_work: 0.3544 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19033 Z= 0.170 Angle : 0.590 10.626 25692 Z= 0.301 Chirality : 0.041 0.215 2987 Planarity : 0.005 0.068 3244 Dihedral : 4.085 20.634 2495 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.84 % Allowed : 20.79 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.18), residues: 2291 helix: 1.64 (0.14), residues: 1532 sheet: -0.07 (0.85), residues: 44 loop : -1.37 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 25 TYR 0.028 0.002 TYR A 672 PHE 0.017 0.002 PHE F 162 TRP 0.010 0.001 TRP B 33 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00406 (19024) covalent geometry : angle 0.59001 (25692) hydrogen bonds : bond 0.05238 ( 1049) hydrogen bonds : angle 3.90665 ( 3099) metal coordination : bond 0.00524 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 368 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.8032 (t80) cc_final: 0.7716 (t80) REVERT: A 139 TYR cc_start: 0.8161 (t80) cc_final: 0.7547 (t80) REVERT: A 142 ARG cc_start: 0.6819 (OUTLIER) cc_final: 0.4855 (pmt-80) REVERT: A 330 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6648 (tm-30) REVERT: A 368 GLN cc_start: 0.8190 (mm110) cc_final: 0.7831 (mm110) REVERT: A 469 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7183 (mtt) REVERT: A 578 LYS cc_start: 0.8589 (pptt) cc_final: 0.8189 (pttm) REVERT: A 589 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7991 (mt-10) REVERT: A 592 THR cc_start: 0.7208 (OUTLIER) cc_final: 0.6959 (t) REVERT: A 621 THR cc_start: 0.8336 (m) cc_final: 0.8024 (p) REVERT: A 644 LEU cc_start: 0.8200 (mp) cc_final: 0.7960 (mp) REVERT: A 675 TYR cc_start: 0.8058 (t80) cc_final: 0.7758 (t80) REVERT: A 735 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 754 ASP cc_start: 0.8349 (m-30) cc_final: 0.7995 (m-30) REVERT: B 87 TRP cc_start: 0.8694 (t-100) cc_final: 0.8436 (t-100) REVERT: C 46 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 70 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8463 (mttp) REVERT: C 138 LEU cc_start: 0.8330 (mt) cc_final: 0.8018 (mt) REVERT: C 156 ASP cc_start: 0.8016 (m-30) cc_final: 0.7446 (m-30) REVERT: C 194 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8061 (mmm-85) REVERT: C 221 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.6341 (tp30) REVERT: C 226 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: C 366 GLU cc_start: 0.8074 (mp0) cc_final: 0.7673 (mp0) REVERT: C 370 GLU cc_start: 0.7524 (tp30) cc_final: 0.7256 (tp30) REVERT: C 382 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7867 (mtt90) REVERT: C 554 ASP cc_start: 0.7933 (p0) cc_final: 0.7549 (p0) REVERT: C 660 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8237 (mpp80) REVERT: C 863 GLU cc_start: 0.8341 (tp30) cc_final: 0.8001 (tm-30) REVERT: C 890 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7497 (tm-30) REVERT: C 897 GLN cc_start: 0.7881 (tm130) cc_final: 0.7551 (tm130) REVERT: C 971 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8126 (tttm) REVERT: C 1016 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: C 1044 LEU cc_start: 0.8102 (mp) cc_final: 0.7878 (mp) REVERT: C 1057 LYS cc_start: 0.8564 (mttm) cc_final: 0.8338 (mttp) REVERT: C 1075 VAL cc_start: 0.8612 (t) cc_final: 0.8290 (m) REVERT: C 1142 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8333 (tt) REVERT: C 1167 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6590 (tm-30) REVERT: C 1171 GLU cc_start: 0.7382 (mp0) cc_final: 0.6288 (mp0) REVERT: C 1175 SER cc_start: 0.8406 (t) cc_final: 0.7889 (p) REVERT: F 144 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4836 (pp-130) REVERT: F 181 TYR cc_start: 0.7753 (m-80) cc_final: 0.6853 (m-80) outliers start: 81 outliers final: 47 residues processed: 412 average time/residue: 0.5859 time to fit residues: 269.4638 Evaluate side-chains 426 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 366 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 938 LYS Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 217 optimal weight: 0.8980 chunk 160 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 170 optimal weight: 0.3980 chunk 148 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 304 HIS A 361 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN C1169 GLN F 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.156063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129134 restraints weight = 27190.744| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.91 r_work: 0.3561 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19033 Z= 0.143 Angle : 0.580 10.549 25692 Z= 0.296 Chirality : 0.040 0.168 2987 Planarity : 0.005 0.067 3244 Dihedral : 4.037 20.275 2495 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.93 % Allowed : 20.79 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.18), residues: 2291 helix: 1.71 (0.14), residues: 1533 sheet: 0.05 (0.86), residues: 44 loop : -1.37 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 272 TYR 0.029 0.001 TYR A 672 PHE 0.014 0.001 PHE A 95 TRP 0.010 0.001 TRP F 213 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00335 (19024) covalent geometry : angle 0.57959 (25692) hydrogen bonds : bond 0.04725 ( 1049) hydrogen bonds : angle 3.83640 ( 3099) metal coordination : bond 0.00359 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 368 time to evaluate : 0.480 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 52 TYR cc_start: 0.8019 (t80) cc_final: 0.7756 (t80) REVERT: A 139 TYR cc_start: 0.8138 (t80) cc_final: 0.7501 (t80) REVERT: A 142 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.4948 (pmt-80) REVERT: A 330 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 469 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7274 (mtt) REVERT: A 578 LYS cc_start: 0.8576 (pptt) cc_final: 0.8176 (pttm) REVERT: A 589 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7989 (mt-10) REVERT: A 592 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6957 (t) REVERT: A 621 THR cc_start: 0.8280 (m) cc_final: 0.7972 (p) REVERT: A 642 ILE cc_start: 0.8548 (mt) cc_final: 0.8312 (tt) REVERT: A 644 LEU cc_start: 0.8174 (mp) cc_final: 0.7950 (mp) REVERT: A 675 TYR cc_start: 0.8062 (t80) cc_final: 0.7833 (t80) REVERT: A 735 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8235 (mp) REVERT: A 754 ASP cc_start: 0.8357 (m-30) cc_final: 0.8006 (m-30) REVERT: B 47 ASN cc_start: 0.8633 (m110) cc_final: 0.8403 (m-40) REVERT: B 87 TRP cc_start: 0.8690 (t-100) cc_final: 0.8425 (t-100) REVERT: C 46 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 70 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8429 (mttp) REVERT: C 116 GLU cc_start: 0.7629 (tp30) cc_final: 0.7425 (tp30) REVERT: C 138 LEU cc_start: 0.8336 (mt) cc_final: 0.8028 (mt) REVERT: C 156 ASP cc_start: 0.8007 (m-30) cc_final: 0.7432 (m-30) REVERT: C 194 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8046 (mmm-85) REVERT: C 221 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: C 226 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.7153 (m-30) REVERT: C 277 GLN cc_start: 0.7014 (pp30) cc_final: 0.6612 (pp30) REVERT: C 279 PHE cc_start: 0.7514 (t80) cc_final: 0.7234 (t80) REVERT: C 366 GLU cc_start: 0.8052 (mp0) cc_final: 0.7674 (mp0) REVERT: C 370 GLU cc_start: 0.7478 (tp30) cc_final: 0.7214 (tp30) REVERT: C 382 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7827 (mtt90) REVERT: C 554 ASP cc_start: 0.7904 (p0) cc_final: 0.7548 (p0) REVERT: C 660 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8233 (mpp80) REVERT: C 863 GLU cc_start: 0.8352 (tp30) cc_final: 0.7996 (tm-30) REVERT: C 890 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7472 (tm-30) REVERT: C 897 GLN cc_start: 0.7870 (tm130) cc_final: 0.7539 (tm130) REVERT: C 915 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 949 ASN cc_start: 0.8181 (m-40) cc_final: 0.7979 (m-40) REVERT: C 969 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7903 (ttp-170) REVERT: C 971 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8110 (tttm) REVERT: C 1016 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6086 (mt-10) REVERT: C 1044 LEU cc_start: 0.8087 (mp) cc_final: 0.7852 (mp) REVERT: C 1057 LYS cc_start: 0.8474 (mttm) cc_final: 0.8237 (mttp) REVERT: C 1075 VAL cc_start: 0.8600 (t) cc_final: 0.8291 (m) REVERT: C 1142 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8330 (tt) REVERT: C 1144 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7807 (ptm-80) REVERT: C 1167 GLU cc_start: 0.7582 (tm-30) cc_final: 0.6280 (tm-30) REVERT: C 1171 GLU cc_start: 0.7342 (mp0) cc_final: 0.6337 (mp0) REVERT: C 1175 SER cc_start: 0.8383 (t) cc_final: 0.7882 (p) REVERT: D 7 GLN cc_start: 0.2639 (OUTLIER) cc_final: 0.2165 (mm110) REVERT: F 144 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4841 (pp-130) REVERT: F 181 TYR cc_start: 0.7829 (m-80) cc_final: 0.6827 (m-80) outliers start: 83 outliers final: 50 residues processed: 412 average time/residue: 0.5710 time to fit residues: 261.7729 Evaluate side-chains 429 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 364 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 969 ARG Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1114 LYS Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 78 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 135 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 361 ASN A 597 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN C1169 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127507 restraints weight = 27020.798| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.89 r_work: 0.3535 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19033 Z= 0.183 Angle : 0.611 9.833 25692 Z= 0.313 Chirality : 0.041 0.180 2987 Planarity : 0.005 0.075 3244 Dihedral : 4.121 20.646 2495 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.74 % Allowed : 20.93 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.97 (0.18), residues: 2291 helix: 1.53 (0.13), residues: 1545 sheet: 0.34 (0.89), residues: 44 loop : -1.37 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 272 TYR 0.029 0.002 TYR A 672 PHE 0.019 0.002 PHE A 95 TRP 0.010 0.001 TRP B 33 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00440 (19024) covalent geometry : angle 0.61098 (25692) hydrogen bonds : bond 0.05443 ( 1049) hydrogen bonds : angle 3.93693 ( 3099) metal coordination : bond 0.00541 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 369 time to evaluate : 0.664 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 52 TYR cc_start: 0.8016 (t80) cc_final: 0.7720 (t80) REVERT: A 139 TYR cc_start: 0.8196 (t80) cc_final: 0.7385 (t80) REVERT: A 142 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.4891 (pmt-80) REVERT: A 330 GLN cc_start: 0.6919 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 368 GLN cc_start: 0.8147 (mm110) cc_final: 0.7813 (mm110) REVERT: A 469 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7283 (mtt) REVERT: A 578 LYS cc_start: 0.8579 (pptt) cc_final: 0.8316 (pttp) REVERT: A 589 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7966 (mt-10) REVERT: A 592 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.7048 (t) REVERT: A 621 THR cc_start: 0.8354 (m) cc_final: 0.8051 (p) REVERT: A 644 LEU cc_start: 0.8179 (mp) cc_final: 0.7953 (mp) REVERT: A 675 TYR cc_start: 0.8071 (t80) cc_final: 0.7858 (t80) REVERT: A 735 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8231 (mp) REVERT: B 47 ASN cc_start: 0.8615 (m110) cc_final: 0.8396 (m-40) REVERT: B 87 TRP cc_start: 0.8714 (t-100) cc_final: 0.8485 (t-100) REVERT: B 88 LEU cc_start: 0.8593 (mt) cc_final: 0.8375 (mp) REVERT: B 89 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8747 (mtpt) REVERT: C 46 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7286 (mm-30) REVERT: C 70 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8489 (mttp) REVERT: C 105 ILE cc_start: 0.7860 (mm) cc_final: 0.7557 (tp) REVERT: C 138 LEU cc_start: 0.8341 (mt) cc_final: 0.8042 (mt) REVERT: C 156 ASP cc_start: 0.8032 (m-30) cc_final: 0.7454 (m-30) REVERT: C 194 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.8061 (mmm-85) REVERT: C 221 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.6917 (tp30) REVERT: C 226 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: C 255 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7861 (mttp) REVERT: C 277 GLN cc_start: 0.6868 (pp30) cc_final: 0.6533 (pp30) REVERT: C 358 ASP cc_start: 0.7881 (t0) cc_final: 0.7633 (t0) REVERT: C 362 SER cc_start: 0.8159 (t) cc_final: 0.7864 (m) REVERT: C 366 GLU cc_start: 0.8009 (mp0) cc_final: 0.7633 (mp0) REVERT: C 370 GLU cc_start: 0.7505 (tp30) cc_final: 0.7223 (tp30) REVERT: C 382 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7782 (mtt90) REVERT: C 554 ASP cc_start: 0.7906 (p0) cc_final: 0.7548 (p0) REVERT: C 660 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8213 (mpp80) REVERT: C 863 GLU cc_start: 0.8385 (tp30) cc_final: 0.8065 (tm-30) REVERT: C 890 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 897 GLN cc_start: 0.7914 (tm130) cc_final: 0.7591 (tm130) REVERT: C 915 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 971 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8154 (tttm) REVERT: C 1016 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: C 1057 LYS cc_start: 0.8508 (mttm) cc_final: 0.8266 (mttp) REVERT: C 1075 VAL cc_start: 0.8580 (t) cc_final: 0.8247 (m) REVERT: C 1142 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8359 (tt) REVERT: C 1167 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6581 (tm-30) REVERT: C 1171 GLU cc_start: 0.7372 (mp0) cc_final: 0.6372 (mp0) REVERT: C 1175 SER cc_start: 0.8431 (t) cc_final: 0.7921 (p) REVERT: D 7 GLN cc_start: 0.2759 (OUTLIER) cc_final: 0.2363 (mm110) REVERT: F 144 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.4974 (pp-130) outliers start: 79 outliers final: 46 residues processed: 412 average time/residue: 0.5914 time to fit residues: 271.3304 Evaluate side-chains 423 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 362 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1163 LYS Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 230 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 361 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN C1169 GLN C1201 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.154273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127353 restraints weight = 26903.311| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.89 r_work: 0.3532 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19033 Z= 0.187 Angle : 0.618 9.847 25692 Z= 0.317 Chirality : 0.042 0.202 2987 Planarity : 0.005 0.069 3244 Dihedral : 4.147 21.004 2495 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.31 % Allowed : 21.45 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 2291 helix: 1.49 (0.13), residues: 1547 sheet: 0.37 (0.88), residues: 44 loop : -1.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 25 TYR 0.030 0.002 TYR A 672 PHE 0.020 0.002 PHE C 282 TRP 0.012 0.001 TRP F 213 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00454 (19024) covalent geometry : angle 0.61784 (25692) hydrogen bonds : bond 0.05501 ( 1049) hydrogen bonds : angle 3.97285 ( 3099) metal coordination : bond 0.00578 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4582 Ramachandran restraints generated. 2291 Oldfield, 0 Emsley, 2291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 361 time to evaluate : 0.613 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: A 52 TYR cc_start: 0.8037 (t80) cc_final: 0.7725 (t80) REVERT: A 285 ASP cc_start: 0.7834 (p0) cc_final: 0.7588 (p0) REVERT: A 330 GLN cc_start: 0.6925 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 469 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7295 (mtt) REVERT: A 578 LYS cc_start: 0.8589 (pptt) cc_final: 0.8346 (pttp) REVERT: A 589 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7957 (mt-10) REVERT: A 592 THR cc_start: 0.7381 (OUTLIER) cc_final: 0.7132 (t) REVERT: A 621 THR cc_start: 0.8362 (m) cc_final: 0.8095 (p) REVERT: A 644 LEU cc_start: 0.8216 (mp) cc_final: 0.7995 (mp) REVERT: A 675 TYR cc_start: 0.8071 (t80) cc_final: 0.7849 (t80) REVERT: A 735 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8227 (mp) REVERT: B 47 ASN cc_start: 0.8608 (m110) cc_final: 0.8394 (m-40) REVERT: B 87 TRP cc_start: 0.8734 (t-100) cc_final: 0.8506 (t-100) REVERT: B 88 LEU cc_start: 0.8624 (mt) cc_final: 0.8408 (mp) REVERT: B 89 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8752 (mtpt) REVERT: C 46 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7279 (mm-30) REVERT: C 70 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8512 (mttp) REVERT: C 104 ASP cc_start: 0.7903 (m-30) cc_final: 0.7622 (m-30) REVERT: C 105 ILE cc_start: 0.7888 (mm) cc_final: 0.7601 (tp) REVERT: C 138 LEU cc_start: 0.8381 (mt) cc_final: 0.8064 (mt) REVERT: C 156 ASP cc_start: 0.8053 (m-30) cc_final: 0.7477 (m-30) REVERT: C 194 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8093 (mmm-85) REVERT: C 221 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: C 226 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: C 255 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7874 (mttp) REVERT: C 277 GLN cc_start: 0.6737 (pp30) cc_final: 0.6276 (pp30) REVERT: C 280 GLU cc_start: 0.6821 (tm-30) cc_final: 0.6477 (pp20) REVERT: C 304 TYR cc_start: 0.8281 (t80) cc_final: 0.8062 (t80) REVERT: C 366 GLU cc_start: 0.7988 (mp0) cc_final: 0.7615 (mp0) REVERT: C 370 GLU cc_start: 0.7513 (tp30) cc_final: 0.7283 (tp30) REVERT: C 382 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7758 (mtt90) REVERT: C 554 ASP cc_start: 0.7901 (p0) cc_final: 0.7554 (p0) REVERT: C 660 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8211 (mpp80) REVERT: C 863 GLU cc_start: 0.8391 (tp30) cc_final: 0.8108 (tm-30) REVERT: C 890 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7450 (tm-30) REVERT: C 897 GLN cc_start: 0.7913 (tm130) cc_final: 0.7599 (tm130) REVERT: C 915 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7567 (tm-30) REVERT: C 971 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8157 (tttm) REVERT: C 1016 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: C 1057 LYS cc_start: 0.8496 (mttm) cc_final: 0.8266 (mttp) REVERT: C 1075 VAL cc_start: 0.8591 (t) cc_final: 0.8211 (m) REVERT: C 1142 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8354 (tt) REVERT: C 1167 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6571 (tm-30) REVERT: C 1169 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: C 1171 GLU cc_start: 0.7355 (mp0) cc_final: 0.6358 (mp0) REVERT: C 1175 SER cc_start: 0.8416 (t) cc_final: 0.7924 (p) REVERT: D 7 GLN cc_start: 0.2776 (OUTLIER) cc_final: 0.2356 (mm110) REVERT: F 144 MET cc_start: 0.5368 (OUTLIER) cc_final: 0.5009 (pp-130) REVERT: F 177 MET cc_start: 0.6525 (tpt) cc_final: 0.6301 (tpp) outliers start: 70 outliers final: 50 residues processed: 394 average time/residue: 0.6159 time to fit residues: 269.4315 Evaluate side-chains 422 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 357 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 660 ARG Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 823 GLN Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 938 LYS Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1016 GLU Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1169 GLN Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain C residue 1201 GLN Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 222 MET Chi-restraints excluded: chain F residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 102 optimal weight: 0.3980 chunk 217 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 169 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 0.0970 chunk 200 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 361 ASN A 597 ASN A 694 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN C1201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127580 restraints weight = 27170.172| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.90 r_work: 0.3534 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.183 19033 Z= 0.229 Angle : 0.910 59.200 25692 Z= 0.529 Chirality : 0.041 0.269 2987 Planarity : 0.005 0.068 3244 Dihedral : 4.190 29.106 2495 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.22 % Allowed : 21.64 % Favored : 75.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.92 (0.18), residues: 2291 helix: 1.51 (0.13), residues: 1547 sheet: 0.37 (0.88), residues: 44 loop : -1.44 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 25 TYR 0.034 0.002 TYR A 139 PHE 0.019 0.002 PHE C 282 TRP 0.012 0.001 TRP F 213 HIS 0.015 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00499 (19024) covalent geometry : angle 0.90968 (25692) hydrogen bonds : bond 0.05395 ( 1049) hydrogen bonds : angle 3.97315 ( 3099) metal coordination : bond 0.00385 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7070.88 seconds wall clock time: 120 minutes 43.40 seconds (7243.40 seconds total)