Starting phenix.real_space_refine on Wed Jan 22 13:57:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8or3_17116/01_2025/8or3_17116.cif Found real_map, /net/cci-nas-00/data/ceres_data/8or3_17116/01_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_17116/01_2025/8or3_17116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8or3_17116/01_2025/8or3_17116.map" model { file = "/net/cci-nas-00/data/ceres_data/8or3_17116/01_2025/8or3_17116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8or3_17116/01_2025/8or3_17116.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.13, per 1000 atoms: 0.54 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: 4.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.90 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: 5.93 Time building geometry restraints manager: 5.09 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: 1.680 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 42.240 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.660 ------------------------------------------------------------------------------- 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 19024 Z= 0.340 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (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 TRP 0.010 0.001 TRP F 213 HIS 0.002 0.000 HIS C 293 PHE 0.034 0.001 PHE C 24 TYR 0.024 0.001 TYR A 52 ARG 0.009 0.000 ARG C 23 *********************** 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 : 2.290 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: 1.5187 time to fit residues: 588.1827 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 : 2.211 ------------------------------------------------------------------------------- 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 195 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 134 optimal weight: 0.0470 chunk 209 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 C1140 GLN D 158 GLN F 183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.161913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135276 restraints weight = 27590.008| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.94 r_work: 0.3634 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19024 Z= 0.239 Angle : 0.582 8.486 25692 Z= 0.300 Chirality : 0.040 0.166 2987 Planarity : 0.005 0.072 3244 Dihedral : 4.878 65.246 2521 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.98 % Allowed : 16.43 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.18), residues: 2291 helix: 1.88 (0.14), residues: 1539 sheet: -0.52 (0.86), residues: 44 loop : -1.17 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 35 HIS 0.004 0.001 HIS C1108 PHE 0.020 0.002 PHE A 402 TYR 0.019 0.002 TYR A 675 ARG 0.005 0.001 ARG A 25 *********************** 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 428 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7463 (tpp80) cc_final: 0.7223 (tpp80) REVERT: A 469 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7304 (mtt) REVERT: A 494 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7747 (tp40) REVERT: A 675 TYR cc_start: 0.7893 (t80) cc_final: 0.7600 (t80) REVERT: A 677 ASN cc_start: 0.7998 (t0) cc_final: 0.7751 (t0) REVERT: A 679 LYS cc_start: 0.7694 (mppt) cc_final: 0.7478 (mppt) REVERT: A 698 THR cc_start: 0.8334 (m) cc_final: 0.8104 (p) REVERT: A 754 ASP cc_start: 0.8254 (m-30) cc_final: 0.7957 (m-30) REVERT: A 768 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: C 15 MET cc_start: 0.8339 (ttm) cc_final: 0.8023 (mtt) REVERT: C 46 GLU cc_start: 0.7175 (mp0) cc_final: 0.6543 (mp0) REVERT: C 70 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: C 138 LEU cc_start: 0.8454 (mt) cc_final: 0.8211 (mt) REVERT: C 156 ASP cc_start: 0.8047 (m-30) cc_final: 0.7650 (m-30) REVERT: C 194 ARG cc_start: 0.8260 (mtt180) cc_final: 0.8053 (mmm-85) REVERT: C 691 ASP cc_start: 0.7676 (p0) cc_final: 0.7395 (p0) REVERT: C 813 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5957 (mm-30) REVERT: C 890 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 897 GLN cc_start: 0.7933 (tm130) cc_final: 0.7603 (tm130) REVERT: C 915 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7506 (tm-30) REVERT: C 1044 LEU cc_start: 0.8107 (mt) cc_final: 0.7793 (mp) REVERT: C 1167 GLU cc_start: 0.7612 (tm-30) cc_final: 0.6986 (tm-30) REVERT: C 1168 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7904 (tttt) REVERT: C 1169 GLN cc_start: 0.7492 (pm20) cc_final: 0.6881 (mp10) REVERT: C 1171 GLU cc_start: 0.7452 (mp0) cc_final: 0.6981 (mp0) REVERT: C 1177 MET cc_start: 0.8303 (mmm) cc_final: 0.8101 (tpt) outliers start: 63 outliers final: 19 residues processed: 396 average time/residue: 1.3940 time to fit residues: 619.2508 Evaluate side-chains 371 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 348 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 469 MET 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 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 253 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 679 LYS Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 1125 LEU Chi-restraints excluded: chain C residue 1163 LYS Chi-restraints excluded: chain C residue 1168 LYS Chi-restraints excluded: chain E residue 192 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 114 optimal weight: 0.0970 chunk 181 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 48 optimal weight: 0.0010 chunk 133 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.161726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135066 restraints weight = 27397.999| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.93 r_work: 0.3644 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19024 Z= 0.182 Angle : 0.528 8.918 25692 Z= 0.269 Chirality : 0.038 0.156 2987 Planarity : 0.004 0.068 3244 Dihedral : 4.022 52.845 2501 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.17 % Allowed : 17.52 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2291 helix: 1.98 (0.14), residues: 1536 sheet: -0.48 (0.85), residues: 44 loop : -1.20 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 213 HIS 0.002 0.000 HIS C 514 PHE 0.020 0.001 PHE A 402 TYR 0.021 0.001 TYR A 672 ARG 0.005 0.000 ARG A 25 *********************** 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 416 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 349 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8319 (mmtp) REVERT: A 330 GLN cc_start: 0.6658 (tm-30) cc_final: 0.6394 (tm-30) REVERT: A 469 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7169 (mtt) REVERT: A 578 LYS cc_start: 0.8450 (pptt) cc_final: 0.8223 (pttm) REVERT: A 621 THR cc_start: 0.8230 (m) cc_final: 0.8010 (p) REVERT: A 675 TYR cc_start: 0.7947 (t80) cc_final: 0.7678 (t80) REVERT: A 677 ASN cc_start: 0.7990 (t0) cc_final: 0.7746 (t0) REVERT: A 679 LYS cc_start: 0.7610 (mppt) cc_final: 0.7358 (mppt) REVERT: A 688 MET cc_start: 0.7345 (mtt) cc_final: 0.7101 (mtt) REVERT: A 735 LEU cc_start: 0.8644 (mt) cc_final: 0.8386 (mp) REVERT: C 46 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6523 (mp0) REVERT: C 70 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8390 (mttp) REVERT: C 138 LEU cc_start: 0.8444 (mt) cc_final: 0.8198 (mt) REVERT: C 156 ASP cc_start: 0.8011 (m-30) cc_final: 0.7526 (m-30) REVERT: C 194 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7956 (mmm-85) REVERT: C 216 GLU cc_start: 0.7559 (mp0) cc_final: 0.7212 (mp0) REVERT: C 221 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.6781 (tp30) REVERT: C 358 ASP cc_start: 0.7780 (t0) cc_final: 0.7552 (t0) REVERT: C 362 SER cc_start: 0.8224 (t) cc_final: 0.7871 (m) REVERT: C 557 SER cc_start: 0.8479 (t) cc_final: 0.8274 (p) REVERT: C 691 ASP cc_start: 0.7661 (p0) cc_final: 0.7192 (p0) REVERT: C 890 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7424 (tm-30) REVERT: C 897 GLN cc_start: 0.7919 (tm130) cc_final: 0.7593 (tm130) REVERT: C 915 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7486 (tm-30) REVERT: C 1044 LEU cc_start: 0.8110 (mt) cc_final: 0.7810 (mp) REVERT: C 1075 VAL cc_start: 0.8685 (t) cc_final: 0.8356 (m) REVERT: C 1167 GLU cc_start: 0.7679 (tm-30) cc_final: 0.6824 (tm-30) REVERT: C 1169 GLN cc_start: 0.7386 (pm20) cc_final: 0.6731 (mp10) REVERT: C 1171 GLU cc_start: 0.7377 (mp0) cc_final: 0.6565 (mp0) REVERT: C 1177 MET cc_start: 0.8296 (mmm) cc_final: 0.8077 (tpt) REVERT: D 7 GLN cc_start: 0.2535 (OUTLIER) cc_final: 0.2092 (mm110) REVERT: F 144 MET cc_start: 0.5347 (pp-130) cc_final: 0.5076 (pp-130) outliers start: 67 outliers final: 29 residues processed: 384 average time/residue: 1.4124 time to fit residues: 605.2687 Evaluate side-chains 386 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 351 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 317 GLU 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 600 THR Chi-restraints excluded: chain A residue 648 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 46 GLU 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 105 ILE 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 253 LEU 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 661 LYS Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 689 MET Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 1114 LYS 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 F residue 222 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 112 optimal weight: 0.0970 chunk 89 optimal weight: 0.5980 chunk 174 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 HIS A 386 ASN A 683 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.159124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132524 restraints weight = 27245.770| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.90 r_work: 0.3609 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19024 Z= 0.211 Angle : 0.541 9.434 25692 Z= 0.276 Chirality : 0.039 0.157 2987 Planarity : 0.005 0.067 3244 Dihedral : 3.780 18.838 2495 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.60 % Allowed : 18.04 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2291 helix: 1.93 (0.14), residues: 1528 sheet: -0.31 (0.87), residues: 44 loop : -1.19 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 72 HIS 0.004 0.001 HIS B 80 PHE 0.017 0.001 PHE A 402 TYR 0.019 0.001 TYR A 157 ARG 0.009 0.000 ARG C1024 *********************** 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 448 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 372 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8321 (mmtp) REVERT: A 330 GLN cc_start: 0.6924 (tm-30) cc_final: 0.6676 (tm-30) REVERT: A 469 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: A 578 LYS cc_start: 0.8509 (pptt) cc_final: 0.8131 (pttm) REVERT: A 621 THR cc_start: 0.8291 (m) cc_final: 0.8000 (p) REVERT: A 675 TYR cc_start: 0.8011 (t80) cc_final: 0.7789 (t80) REVERT: A 688 MET cc_start: 0.7640 (mtt) cc_final: 0.7418 (mtt) REVERT: A 735 LEU cc_start: 0.8603 (mt) cc_final: 0.8284 (mp) REVERT: B 87 TRP cc_start: 0.8704 (t-100) cc_final: 0.8446 (t-100) REVERT: C 46 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: C 70 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8442 (mttp) REVERT: C 138 LEU cc_start: 0.8440 (mt) cc_final: 0.8177 (mt) REVERT: C 216 GLU cc_start: 0.7574 (mp0) cc_final: 0.7312 (mp0) REVERT: C 221 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7118 (tp30) REVERT: C 262 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8128 (tmtt) REVERT: C 358 ASP cc_start: 0.7778 (t0) cc_final: 0.7537 (t0) REVERT: C 362 SER cc_start: 0.8250 (t) cc_final: 0.7927 (m) REVERT: C 691 ASP cc_start: 0.7755 (p0) cc_final: 0.7341 (p0) REVERT: C 890 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7488 (tm-30) REVERT: C 897 GLN cc_start: 0.7946 (tm130) cc_final: 0.7639 (tm130) REVERT: C 949 ASN cc_start: 0.8237 (m-40) cc_final: 0.7982 (m-40) REVERT: C 1044 LEU cc_start: 0.8167 (mt) cc_final: 0.7885 (mp) REVERT: C 1075 VAL cc_start: 0.8694 (t) cc_final: 0.8375 (m) REVERT: C 1142 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8342 (tt) REVERT: C 1158 LYS cc_start: 0.8139 (tttt) cc_final: 0.7882 (tttt) REVERT: C 1165 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7114 (tp30) REVERT: C 1167 GLU cc_start: 0.7718 (tm-30) cc_final: 0.6933 (tm-30) REVERT: C 1169 GLN cc_start: 0.7438 (pm20) cc_final: 0.6887 (pm20) REVERT: C 1171 GLU cc_start: 0.7406 (mp0) cc_final: 0.6624 (mp0) REVERT: D 7 GLN cc_start: 0.2459 (OUTLIER) cc_final: 0.2063 (mm110) REVERT: F 144 MET cc_start: 0.5349 (pp-130) cc_final: 0.5045 (pp-130) REVERT: F 181 TYR cc_start: 0.7733 (m-80) cc_final: 0.6862 (m-80) outliers start: 76 outliers final: 34 residues processed: 410 average time/residue: 1.4021 time to fit residues: 645.4239 Evaluate side-chains 402 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 362 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 111 MET 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 600 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain B residue 69 THR 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 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 253 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 960 LEU 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 120 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 208 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 187 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 143 HIS A 361 ASN A 386 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN F 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.158005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131354 restraints weight = 27350.358| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.89 r_work: 0.3591 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19024 Z= 0.228 Angle : 0.566 12.330 25692 Z= 0.287 Chirality : 0.040 0.167 2987 Planarity : 0.005 0.067 3244 Dihedral : 3.856 19.374 2495 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.79 % Allowed : 18.56 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2291 helix: 1.89 (0.14), residues: 1525 sheet: -0.28 (0.86), residues: 44 loop : -1.27 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 107 HIS 0.005 0.001 HIS B 80 PHE 0.015 0.001 PHE A 402 TYR 0.025 0.002 TYR A 672 ARG 0.011 0.000 ARG C 743 *********************** 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 459 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 379 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLN cc_start: 0.6886 (tm-30) cc_final: 0.6580 (tm-30) REVERT: A 469 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7194 (mtt) REVERT: A 578 LYS cc_start: 0.8516 (pptt) cc_final: 0.8278 (pttp) REVERT: A 592 THR cc_start: 0.6995 (OUTLIER) cc_final: 0.6724 (t) REVERT: A 621 THR cc_start: 0.8285 (m) cc_final: 0.7963 (p) REVERT: A 688 MET cc_start: 0.7902 (mtt) cc_final: 0.7695 (mtt) REVERT: A 735 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 738 LEU cc_start: 0.8609 (mp) cc_final: 0.8343 (mp) REVERT: A 768 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6122 (tm-30) REVERT: B 87 TRP cc_start: 0.8734 (t-100) cc_final: 0.8500 (t-100) REVERT: C 46 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: C 70 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8452 (mttp) REVERT: C 138 LEU cc_start: 0.8456 (mt) cc_final: 0.8178 (mt) REVERT: C 216 GLU cc_start: 0.7545 (mp0) cc_final: 0.7144 (mp0) REVERT: C 221 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.6667 (tp30) REVERT: C 262 LYS cc_start: 0.8365 (tmtt) cc_final: 0.8148 (tmtt) REVERT: C 362 SER cc_start: 0.8229 (t) cc_final: 0.7916 (m) REVERT: C 382 ARG cc_start: 0.7981 (mtt180) cc_final: 0.7742 (mtt180) REVERT: C 554 ASP cc_start: 0.7909 (p0) cc_final: 0.7602 (p0) REVERT: C 691 ASP cc_start: 0.7769 (p0) cc_final: 0.7327 (p0) REVERT: C 823 GLN cc_start: 0.7224 (mp10) cc_final: 0.7017 (mp10) REVERT: C 890 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7492 (tm-30) REVERT: C 897 GLN cc_start: 0.7913 (tm130) cc_final: 0.7595 (tm130) REVERT: C 915 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 1044 LEU cc_start: 0.8181 (mt) cc_final: 0.7901 (mp) REVERT: C 1075 VAL cc_start: 0.8644 (t) cc_final: 0.8343 (m) REVERT: C 1142 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8344 (tt) REVERT: C 1158 LYS cc_start: 0.8175 (tttt) cc_final: 0.7931 (tttt) REVERT: C 1165 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7090 (tp30) REVERT: C 1167 GLU cc_start: 0.7713 (tm-30) cc_final: 0.6837 (tm-30) REVERT: C 1169 GLN cc_start: 0.7453 (pm20) cc_final: 0.6859 (pm20) REVERT: C 1171 GLU cc_start: 0.7379 (mp0) cc_final: 0.6580 (mp0) REVERT: D 7 GLN cc_start: 0.2571 (OUTLIER) cc_final: 0.2131 (mm110) REVERT: F 144 MET cc_start: 0.5260 (pp-130) cc_final: 0.4948 (pp-130) REVERT: F 181 TYR cc_start: 0.7754 (m-80) cc_final: 0.7081 (m-80) outliers start: 80 outliers final: 42 residues processed: 419 average time/residue: 1.3657 time to fit residues: 640.0805 Evaluate side-chains 417 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 263 LYS Chi-restraints excluded: chain A residue 317 GLU 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 648 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 GLU 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 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 253 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 647 VAL 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 957 LYS Chi-restraints excluded: chain C residue 960 LEU 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 100 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 208 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 162 optimal weight: 2.9990 chunk 144 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 171 optimal weight: 0.6980 chunk 112 optimal weight: 0.0970 chunk 132 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN 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** D 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.159070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.132387 restraints weight = 27428.564| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.92 r_work: 0.3605 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19024 Z= 0.182 Angle : 0.538 11.052 25692 Z= 0.273 Chirality : 0.038 0.143 2987 Planarity : 0.004 0.066 3244 Dihedral : 3.787 18.540 2495 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.50 % Allowed : 19.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2291 helix: 1.94 (0.14), residues: 1532 sheet: -0.23 (0.85), residues: 44 loop : -1.29 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 107 HIS 0.006 0.001 HIS C 293 PHE 0.012 0.001 PHE A 402 TYR 0.024 0.001 TYR A 672 ARG 0.007 0.000 ARG A 25 *********************** 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 446 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 372 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.7905 (tp30) cc_final: 0.7688 (tp30) REVERT: A 298 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8338 (mmtp) REVERT: A 330 GLN cc_start: 0.6995 (tm-30) cc_final: 0.6674 (tm-30) REVERT: A 469 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7101 (mtt) REVERT: A 578 LYS cc_start: 0.8545 (pptt) cc_final: 0.8290 (pttp) REVERT: A 589 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 621 THR cc_start: 0.8206 (m) cc_final: 0.7796 (p) REVERT: A 735 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 738 LEU cc_start: 0.8560 (mp) cc_final: 0.8301 (mp) REVERT: A 768 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6119 (tm-30) REVERT: B 87 TRP cc_start: 0.8735 (t-100) cc_final: 0.8490 (t-100) REVERT: C 46 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: C 70 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: C 138 LEU cc_start: 0.8425 (mt) cc_final: 0.8141 (mt) REVERT: C 216 GLU cc_start: 0.7542 (mp0) cc_final: 0.7098 (mp0) REVERT: C 221 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: C 362 SER cc_start: 0.8215 (t) cc_final: 0.7892 (m) REVERT: C 366 GLU cc_start: 0.7997 (mp0) cc_final: 0.7628 (mp0) REVERT: C 382 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7706 (mtt180) REVERT: C 554 ASP cc_start: 0.7878 (p0) cc_final: 0.7601 (p0) REVERT: C 691 ASP cc_start: 0.7746 (p0) cc_final: 0.7291 (p0) REVERT: C 823 GLN cc_start: 0.7213 (mp10) cc_final: 0.7006 (mp10) REVERT: C 890 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 897 GLN cc_start: 0.7911 (tm130) cc_final: 0.7586 (tm130) REVERT: C 949 ASN cc_start: 0.8186 (m-40) cc_final: 0.7947 (m-40) REVERT: C 1044 LEU cc_start: 0.8139 (mt) cc_final: 0.7859 (mp) REVERT: C 1075 VAL cc_start: 0.8638 (t) cc_final: 0.8336 (m) REVERT: C 1142 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8306 (tt) REVERT: C 1158 LYS cc_start: 0.8187 (tttt) cc_final: 0.7947 (tttt) REVERT: C 1165 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7120 (tp30) REVERT: C 1167 GLU cc_start: 0.7682 (tm-30) cc_final: 0.6829 (tm-30) REVERT: C 1169 GLN cc_start: 0.7442 (pm20) cc_final: 0.6835 (pm20) REVERT: C 1171 GLU cc_start: 0.7371 (mp0) cc_final: 0.6565 (mp0) REVERT: D 7 GLN cc_start: 0.2647 (OUTLIER) cc_final: 0.2340 (mm110) REVERT: F 144 MET cc_start: 0.5377 (pp-130) cc_final: 0.4992 (pp-130) REVERT: F 181 TYR cc_start: 0.7739 (m-80) cc_final: 0.7023 (m-80) outliers start: 74 outliers final: 38 residues processed: 410 average time/residue: 1.3907 time to fit residues: 635.4902 Evaluate side-chains 416 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 370 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET 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 616 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 GLU 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 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 221 GLU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 306 THR 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 647 VAL 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 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 106 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 222 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 200 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 134 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 213 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A 386 ASN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.156610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129437 restraints weight = 27176.064| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.99 r_work: 0.3557 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19024 Z= 0.243 Angle : 0.584 10.420 25692 Z= 0.296 Chirality : 0.040 0.163 2987 Planarity : 0.005 0.066 3244 Dihedral : 3.864 19.953 2495 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.65 % Allowed : 19.41 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2291 helix: 1.85 (0.14), residues: 1532 sheet: -0.11 (0.83), residues: 44 loop : -1.31 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 107 HIS 0.004 0.001 HIS A 524 PHE 0.013 0.001 PHE A 402 TYR 0.018 0.002 TYR A 157 ARG 0.008 0.000 ARG A 25 *********************** 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 455 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 378 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.7885 (tp30) cc_final: 0.7669 (tp30) REVERT: A 143 HIS cc_start: 0.5859 (OUTLIER) cc_final: 0.5584 (m-70) REVERT: A 298 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8328 (mmtp) REVERT: A 330 GLN cc_start: 0.6911 (tm-30) cc_final: 0.6575 (tm-30) REVERT: A 469 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7287 (mtt) REVERT: A 578 LYS cc_start: 0.8566 (pptt) cc_final: 0.8145 (pttm) REVERT: A 589 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7893 (mt-10) REVERT: A 621 THR cc_start: 0.8253 (m) cc_final: 0.7816 (p) REVERT: A 644 LEU cc_start: 0.8251 (mp) cc_final: 0.8007 (mp) REVERT: A 735 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 738 LEU cc_start: 0.8583 (mp) cc_final: 0.8332 (OUTLIER) REVERT: A 768 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6119 (tm-30) REVERT: B 87 TRP cc_start: 0.8686 (t-100) cc_final: 0.8439 (t-100) REVERT: C 46 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: C 70 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: C 138 LEU cc_start: 0.8357 (mt) cc_final: 0.8078 (mt) REVERT: C 216 GLU cc_start: 0.7573 (mp0) cc_final: 0.7204 (mp0) REVERT: C 221 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.6428 (tp30) REVERT: C 362 SER cc_start: 0.8158 (t) cc_final: 0.7826 (m) REVERT: C 366 GLU cc_start: 0.7972 (mp0) cc_final: 0.7596 (mp0) REVERT: C 554 ASP cc_start: 0.7869 (p0) cc_final: 0.7516 (p0) REVERT: C 660 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (mpp80) REVERT: C 691 ASP cc_start: 0.7834 (p0) cc_final: 0.7369 (p0) REVERT: C 890 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 897 GLN cc_start: 0.7886 (tm130) cc_final: 0.7581 (tm130) REVERT: C 949 ASN cc_start: 0.8185 (m-40) cc_final: 0.7926 (m-40) REVERT: C 1044 LEU cc_start: 0.8124 (mt) cc_final: 0.7851 (mp) REVERT: C 1057 LYS cc_start: 0.8580 (mttm) cc_final: 0.8333 (mttp) REVERT: C 1075 VAL cc_start: 0.8587 (t) cc_final: 0.8274 (m) REVERT: C 1142 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8270 (tt) REVERT: C 1158 LYS cc_start: 0.8197 (tttt) cc_final: 0.7968 (tttt) REVERT: C 1165 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7171 (tp30) REVERT: C 1167 GLU cc_start: 0.7661 (tm-30) cc_final: 0.6780 (tm-30) REVERT: C 1169 GLN cc_start: 0.7463 (pm20) cc_final: 0.6848 (pm20) REVERT: C 1171 GLU cc_start: 0.7470 (mp0) cc_final: 0.6382 (mp0) REVERT: C 1175 SER cc_start: 0.8465 (t) cc_final: 0.7939 (p) REVERT: D 7 GLN cc_start: 0.2689 (OUTLIER) cc_final: 0.2339 (mm110) REVERT: F 144 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4856 (pp-130) REVERT: F 181 TYR cc_start: 0.7690 (m-80) cc_final: 0.6873 (m-80) outliers start: 77 outliers final: 45 residues processed: 416 average time/residue: 1.4103 time to fit residues: 654.5861 Evaluate side-chains 427 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 372 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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 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 600 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 GLU 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 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 280 GLU Chi-restraints excluded: chain C residue 306 THR 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 735 LEU Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 957 LYS Chi-restraints excluded: chain C residue 960 LEU 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 106 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 208 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 204 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 0.0050 chunk 175 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 126 optimal weight: 0.0060 overall best weight: 0.3610 ------------------------------------------------------------------------------- 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 386 ASN A 597 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.158591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.131582 restraints weight = 27226.304| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.98 r_work: 0.3586 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19024 Z= 0.178 Angle : 0.559 10.466 25692 Z= 0.283 Chirality : 0.038 0.181 2987 Planarity : 0.004 0.065 3244 Dihedral : 3.796 19.302 2495 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.41 % Allowed : 19.98 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 2291 helix: 1.98 (0.14), residues: 1531 sheet: 0.02 (0.84), residues: 44 loop : -1.32 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 33 HIS 0.003 0.001 HIS A 143 PHE 0.014 0.001 PHE C 282 TYR 0.026 0.001 TYR A 672 ARG 0.006 0.000 ARG C1024 *********************** 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 435 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 363 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8541 (ttp) cc_final: 0.8217 (ttm) REVERT: A 108 GLU cc_start: 0.7916 (tp30) cc_final: 0.7703 (tp30) REVERT: A 143 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5611 (m-70) REVERT: A 298 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8378 (mtpp) REVERT: A 330 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6538 (tm-30) REVERT: A 469 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7211 (mtt) REVERT: A 578 LYS cc_start: 0.8563 (pptt) cc_final: 0.8340 (pttp) REVERT: A 589 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 621 THR cc_start: 0.8203 (m) cc_final: 0.7782 (p) REVERT: A 642 ILE cc_start: 0.8503 (mt) cc_final: 0.8299 (tt) REVERT: A 644 LEU cc_start: 0.8251 (mp) cc_final: 0.8010 (mp) REVERT: A 735 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 738 LEU cc_start: 0.8534 (mp) cc_final: 0.8282 (mp) REVERT: A 768 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6078 (tm-30) REVERT: B 87 TRP cc_start: 0.8678 (t-100) cc_final: 0.8415 (t-100) REVERT: C 44 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6171 (t0) REVERT: C 46 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: C 70 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (mttp) REVERT: C 138 LEU cc_start: 0.8369 (mt) cc_final: 0.8069 (mt) REVERT: C 216 GLU cc_start: 0.7616 (mp0) cc_final: 0.7273 (mp0) REVERT: C 221 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.6580 (tp30) REVERT: C 279 PHE cc_start: 0.7553 (t80) cc_final: 0.7302 (t80) REVERT: C 362 SER cc_start: 0.8188 (t) cc_final: 0.7842 (m) REVERT: C 366 GLU cc_start: 0.7986 (mp0) cc_final: 0.7595 (mp0) REVERT: C 382 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7666 (mtt90) REVERT: C 554 ASP cc_start: 0.7854 (p0) cc_final: 0.7508 (p0) REVERT: C 691 ASP cc_start: 0.7821 (p0) cc_final: 0.7409 (p0) REVERT: C 890 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7463 (tm-30) REVERT: C 897 GLN cc_start: 0.7879 (tm130) cc_final: 0.7585 (tm130) REVERT: C 971 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8231 (tmtp) REVERT: C 1057 LYS cc_start: 0.8509 (mttm) cc_final: 0.8255 (mttp) REVERT: C 1075 VAL cc_start: 0.8578 (t) cc_final: 0.8278 (m) REVERT: C 1142 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8223 (tt) REVERT: C 1158 LYS cc_start: 0.8159 (tttt) cc_final: 0.7931 (tttt) REVERT: C 1165 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7176 (tp30) REVERT: C 1167 GLU cc_start: 0.7686 (tm-30) cc_final: 0.6796 (tm-30) REVERT: C 1169 GLN cc_start: 0.7457 (pm20) cc_final: 0.6842 (pm20) REVERT: C 1171 GLU cc_start: 0.7413 (mp0) cc_final: 0.6383 (mp0) REVERT: C 1175 SER cc_start: 0.8441 (t) cc_final: 0.7917 (p) REVERT: D 7 GLN cc_start: 0.2645 (OUTLIER) cc_final: 0.2338 (mm110) REVERT: F 144 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4861 (pp-130) REVERT: F 181 TYR cc_start: 0.7649 (m-80) cc_final: 0.6953 (m-80) outliers start: 72 outliers final: 40 residues processed: 402 average time/residue: 1.4281 time to fit residues: 639.9326 Evaluate side-chains 410 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 358 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 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 488 MET 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 648 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 GLU 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 44 ASP 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 170 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 306 THR 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 684 SER Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 767 THR Chi-restraints excluded: chain C residue 957 LYS Chi-restraints excluded: chain C residue 960 LEU 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 100 LEU Chi-restraints excluded: chain E residue 106 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 208 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 386 ASN A 538 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.152356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125322 restraints weight = 27204.805| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.89 r_work: 0.3499 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 19024 Z= 0.468 Angle : 0.705 10.601 25692 Z= 0.358 Chirality : 0.047 0.262 2987 Planarity : 0.005 0.070 3244 Dihedral : 4.307 21.528 2495 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.22 % Allowed : 20.45 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2291 helix: 1.38 (0.13), residues: 1540 sheet: 1.57 (0.95), residues: 34 loop : -1.39 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 35 HIS 0.009 0.001 HIS A 524 PHE 0.024 0.003 PHE A 95 TYR 0.032 0.003 TYR A 157 ARG 0.009 0.001 ARG C 743 *********************** 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 451 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 383 time to evaluate : 2.146 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 261 MET cc_start: 0.8745 (mtt) cc_final: 0.8416 (mtp) REVERT: A 298 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8336 (mmtp) REVERT: A 368 GLN cc_start: 0.8198 (mm110) cc_final: 0.7840 (mm110) REVERT: A 469 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7364 (mtt) REVERT: A 489 ILE cc_start: 0.8460 (mm) cc_final: 0.8244 (mp) REVERT: A 578 LYS cc_start: 0.8602 (pptt) cc_final: 0.8358 (pttp) REVERT: A 621 THR cc_start: 0.8412 (m) cc_final: 0.8086 (p) REVERT: A 644 LEU cc_start: 0.8262 (mp) cc_final: 0.8015 (mp) REVERT: A 693 LYS cc_start: 0.7575 (ttmm) cc_final: 0.7365 (ttmm) REVERT: A 735 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8213 (mt) REVERT: A 738 LEU cc_start: 0.8689 (mp) cc_final: 0.8465 (mp) REVERT: A 754 ASP cc_start: 0.8391 (m-30) cc_final: 0.8022 (m-30) REVERT: A 768 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6089 (tm-30) REVERT: B 47 ASN cc_start: 0.8646 (m110) cc_final: 0.8421 (m-40) REVERT: B 87 TRP cc_start: 0.8729 (t-100) cc_final: 0.8467 (t-100) REVERT: C 44 ASP cc_start: 0.6727 (t70) cc_final: 0.6505 (t0) REVERT: C 70 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8591 (mttp) REVERT: C 104 ASP cc_start: 0.7879 (m-30) cc_final: 0.7647 (m-30) REVERT: C 105 ILE cc_start: 0.7981 (mm) cc_final: 0.7723 (tp) REVERT: C 138 LEU cc_start: 0.8385 (mt) cc_final: 0.8098 (mt) REVERT: C 221 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: C 255 LYS cc_start: 0.8150 (mttt) cc_final: 0.7889 (mttp) REVERT: C 279 PHE cc_start: 0.7743 (t80) cc_final: 0.7381 (t80) REVERT: C 304 TYR cc_start: 0.8338 (t80) cc_final: 0.8089 (t80) REVERT: C 506 CYS cc_start: 0.8320 (t) cc_final: 0.8065 (m) REVERT: C 554 ASP cc_start: 0.7884 (p0) cc_final: 0.7554 (p0) REVERT: C 721 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7706 (mttp) REVERT: C 863 GLU cc_start: 0.8358 (tp30) cc_final: 0.8120 (tm-30) REVERT: C 890 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7485 (tm-30) REVERT: C 897 GLN cc_start: 0.7921 (tm130) cc_final: 0.7620 (tm130) REVERT: C 971 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8151 (tttm) REVERT: C 1057 LYS cc_start: 0.8605 (mttm) cc_final: 0.8386 (mttp) REVERT: C 1065 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6703 (tm-30) REVERT: C 1075 VAL cc_start: 0.8575 (t) cc_final: 0.8215 (m) REVERT: C 1142 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8323 (tt) REVERT: C 1167 GLU cc_start: 0.7607 (tm-30) cc_final: 0.6716 (tm-30) REVERT: C 1171 GLU cc_start: 0.7485 (mp0) cc_final: 0.6508 (mp0) REVERT: C 1177 MET cc_start: 0.8362 (mmm) cc_final: 0.8135 (tpp) REVERT: F 144 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4832 (pp-130) outliers start: 68 outliers final: 39 residues processed: 420 average time/residue: 1.4547 time to fit residues: 681.4789 Evaluate side-chains 415 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 368 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 257 VAL 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 616 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 684 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 GLU 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 15 MET 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 218 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 79 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 386 ASN A 597 ASN A 694 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 GLN D 7 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128324 restraints weight = 26926.286| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.91 r_work: 0.3544 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19024 Z= 0.254 Angle : 0.627 10.470 25692 Z= 0.320 Chirality : 0.041 0.239 2987 Planarity : 0.005 0.068 3244 Dihedral : 4.166 21.494 2495 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.46 % Allowed : 21.54 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2291 helix: 1.56 (0.13), residues: 1535 sheet: 0.47 (0.90), residues: 44 loop : -1.40 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 144 HIS 0.010 0.001 HIS A 143 PHE 0.022 0.002 PHE C 282 TYR 0.031 0.002 TYR A 672 ARG 0.009 0.000 ARG A 25 ********************** 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 423 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 371 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8654 (ttp) cc_final: 0.8427 (ttp) REVERT: A 52 TYR cc_start: 0.7816 (t80) cc_final: 0.7587 (t80) REVERT: A 139 TYR cc_start: 0.8207 (t80) cc_final: 0.7310 (t80) REVERT: A 142 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.4790 (pmt-80) REVERT: A 261 MET cc_start: 0.8616 (mtt) cc_final: 0.8220 (mtp) REVERT: A 298 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8310 (mmtp) REVERT: A 330 GLN cc_start: 0.6997 (tm-30) cc_final: 0.6719 (tm-30) REVERT: A 368 GLN cc_start: 0.8164 (mm110) cc_final: 0.7811 (mm110) REVERT: A 469 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7207 (mtt) REVERT: A 578 LYS cc_start: 0.8571 (pptt) cc_final: 0.8178 (pttm) REVERT: A 589 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 621 THR cc_start: 0.8369 (m) cc_final: 0.8032 (p) REVERT: A 642 ILE cc_start: 0.8580 (mt) cc_final: 0.8340 (tt) REVERT: A 644 LEU cc_start: 0.8247 (mp) cc_final: 0.8016 (mp) REVERT: A 735 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 738 LEU cc_start: 0.8622 (mp) cc_final: 0.8386 (mp) REVERT: A 768 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6052 (tm-30) REVERT: B 87 TRP cc_start: 0.8708 (t-100) cc_final: 0.8449 (t-100) REVERT: C 15 MET cc_start: 0.8630 (ttm) cc_final: 0.8261 (mtt) REVERT: C 46 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 70 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8498 (mttp) REVERT: C 104 ASP cc_start: 0.7892 (m-30) cc_final: 0.7642 (m-30) REVERT: C 138 LEU cc_start: 0.8367 (mt) cc_final: 0.8081 (mt) REVERT: C 221 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.6882 (tp30) REVERT: C 255 LYS cc_start: 0.8151 (mttt) cc_final: 0.7891 (mttp) REVERT: C 279 PHE cc_start: 0.7672 (t80) cc_final: 0.7331 (t80) REVERT: C 382 ARG cc_start: 0.7981 (mtt90) cc_final: 0.7693 (mtp85) REVERT: C 554 ASP cc_start: 0.7856 (p0) cc_final: 0.7506 (p0) REVERT: C 721 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7594 (mttp) REVERT: C 863 GLU cc_start: 0.8343 (tp30) cc_final: 0.8116 (tm-30) REVERT: C 890 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7439 (tm-30) REVERT: C 897 GLN cc_start: 0.7952 (tm130) cc_final: 0.7636 (tm130) REVERT: C 915 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7585 (tm-30) REVERT: C 971 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8148 (tttm) REVERT: C 1057 LYS cc_start: 0.8476 (mttm) cc_final: 0.8228 (mttp) REVERT: C 1065 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6709 (tm-30) REVERT: C 1075 VAL cc_start: 0.8578 (t) cc_final: 0.8209 (m) REVERT: C 1142 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (tt) REVERT: C 1144 ARG cc_start: 0.8047 (ptm160) cc_final: 0.7847 (ptm-80) REVERT: C 1158 LYS cc_start: 0.8249 (tttt) cc_final: 0.7968 (tttt) REVERT: C 1167 GLU cc_start: 0.7595 (tm-30) cc_final: 0.6571 (tm-30) REVERT: C 1171 GLU cc_start: 0.7428 (mp0) cc_final: 0.6283 (mp0) REVERT: C 1175 SER cc_start: 0.8435 (t) cc_final: 0.7923 (p) REVERT: C 1177 MET cc_start: 0.8273 (mmm) cc_final: 0.8066 (tpp) REVERT: F 144 MET cc_start: 0.5308 (OUTLIER) cc_final: 0.4874 (pp-130) outliers start: 52 outliers final: 37 residues processed: 396 average time/residue: 1.4669 time to fit residues: 645.9103 Evaluate side-chains 410 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 364 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 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 616 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 768 GLU 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 79 VAL Chi-restraints excluded: chain C residue 170 VAL 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 280 GLU Chi-restraints excluded: chain C residue 306 THR 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 684 SER Chi-restraints excluded: chain C residue 755 MET Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 971 LYS Chi-restraints excluded: chain C residue 1142 LEU Chi-restraints excluded: chain C residue 1194 LEU Chi-restraints excluded: chain C residue 1201 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 145 GLU Chi-restraints excluded: chain F residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 142 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS ** A 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 564 GLN A 694 GLN ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN ** C1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128224 restraints weight = 27102.549| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.94 r_work: 0.3538 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 19024 Z= 0.326 Angle : 0.908 59.138 25692 Z= 0.483 Chirality : 0.041 0.327 2987 Planarity : 0.005 0.068 3244 Dihedral : 4.180 21.515 2495 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.56 % Allowed : 21.83 % Favored : 75.62 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2291 helix: 1.56 (0.13), residues: 1535 sheet: 0.47 (0.90), residues: 44 loop : -1.42 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 213 HIS 0.009 0.001 HIS A 143 PHE 0.020 0.002 PHE C 282 TYR 0.064 0.002 TYR A 52 ARG 0.009 0.000 ARG A 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16462.51 seconds wall clock time: 291 minutes 41.28 seconds (17501.28 seconds total)