Starting phenix.real_space_refine on Fri Mar 6 08:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c4j_30285/03_2026/7c4j_30285.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c4j_30285/03_2026/7c4j_30285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c4j_30285/03_2026/7c4j_30285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c4j_30285/03_2026/7c4j_30285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c4j_30285/03_2026/7c4j_30285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c4j_30285/03_2026/7c4j_30285.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 19026 2.51 5 N 5085 2.21 5 O 5570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 257 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29757 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3048 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 15, 'TRANS': 358} Chain breaks: 6 Chain: "B" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3250 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 4 Chain: "C" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1266 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 3 Chain: "D" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3445 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 24, 'TRANS': 396} Chain breaks: 3 Chain: "E" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2355 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 15, 'TRANS': 272} Chain breaks: 7 Chain: "F" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3134 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 19, 'TRANS': 363} Chain breaks: 1 Chain: "H" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1966 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 10, 'TRANS': 231} Chain: "I" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4242 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 24, 'TRANS': 499} Chain breaks: 8 Chain: "G" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 209 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 23, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 62 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 482 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain breaks: 3 Chain: "K" Number of atoms: 3131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 387, 3111 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 Conformer: "B" Number of residues, atoms: 387, 3111 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 19, 'TRANS': 367} Chain breaks: 14 bond proxies already assigned to first conformer: 3145 Chain: "L" Number of atoms: 3167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 3160 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 17, 'TRANS': 374} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 392, 3160 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 17, 'TRANS': 374} Chain breaks: 5 bond proxies already assigned to first conformer: 3214 Time building chain proxies: 7.28, per 1000 atoms: 0.24 Number of scatterers: 29757 At special positions: 0 Unit cell: (175.007, 228.27, 155.441, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 5570 8.00 N 5085 7.00 C 19026 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 Links applied TRANS " UNK G 125 " - " HIS G 124 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 25 sheets defined 57.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.965A pdb=" N MET A 59 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 Processing helix chain 'A' and resid 69 through 106 removed outlier: 4.361A pdb=" N TYR A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.890A pdb=" N PHE A 181 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 182 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 403 through 415 removed outlier: 4.568A pdb=" N LEU A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.501A pdb=" N THR A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 510 Proline residue: A 478 - end of helix removed outlier: 3.516A pdb=" N ASP A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 530 Processing helix chain 'A' and resid 536 through 541 Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.732A pdb=" N LYS B 312 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.652A pdb=" N ALA B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 419 through 423 removed outlier: 4.040A pdb=" N LEU B 422 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE B 423 " --> pdb=" O ARG B 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 419 through 423' Processing helix chain 'B' and resid 437 through 444 Processing helix chain 'B' and resid 451 through 468 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.699A pdb=" N GLU B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 542 Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.624A pdb=" N LEU B 592 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.868A pdb=" N SER B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 610 " --> pdb=" O PRO B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 640 Processing helix chain 'B' and resid 673 through 741 removed outlier: 3.768A pdb=" N ARG B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 678 " --> pdb=" O ASN B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 776 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.631A pdb=" N VAL C 83 " --> pdb=" O ASP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 123 removed outlier: 3.592A pdb=" N ASN C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 154 Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.510A pdb=" N ALA C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 177 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.544A pdb=" N LYS C 216 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 244 removed outlier: 3.828A pdb=" N ASP C 235 " --> pdb=" O HIS C 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 312 No H-bonds generated for 'chain 'D' and resid 310 through 312' Processing helix chain 'D' and resid 321 through 327 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 363 through 371 removed outlier: 3.739A pdb=" N ALA D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 removed outlier: 3.554A pdb=" N LEU D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 444 Processing helix chain 'D' and resid 447 through 469 removed outlier: 3.706A pdb=" N HIS D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 524 removed outlier: 4.046A pdb=" N ASP D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 542 removed outlier: 3.535A pdb=" N GLN D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 554 Processing helix chain 'D' and resid 557 through 566 Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.890A pdb=" N LYS D 593 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 616 Processing helix chain 'D' and resid 619 through 627 removed outlier: 3.607A pdb=" N VAL D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 648 through 747 removed outlier: 3.672A pdb=" N HIS D 652 " --> pdb=" O LYS D 648 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 653 " --> pdb=" O PRO D 649 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 697 " --> pdb=" O LYS D 693 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS D 702 " --> pdb=" O LEU D 698 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS D 703 " --> pdb=" O ASN D 699 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU D 704 " --> pdb=" O HIS D 700 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN D 731 " --> pdb=" O LEU D 727 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 732 " --> pdb=" O ASN D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 776 removed outlier: 4.041A pdb=" N LYS D 776 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.666A pdb=" N ILE E 35 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 282 through 296 removed outlier: 3.585A pdb=" N ARG E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 450 through 461 removed outlier: 3.863A pdb=" N GLU E 456 " --> pdb=" O ASN E 452 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 465 through 502 Processing helix chain 'E' and resid 511 through 525 Processing helix chain 'F' and resid 323 through 327 removed outlier: 4.319A pdb=" N TRP F 327 " --> pdb=" O PRO F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 357 Processing helix chain 'F' and resid 370 through 400 Processing helix chain 'F' and resid 441 through 450 Processing helix chain 'F' and resid 487 through 499 Processing helix chain 'F' and resid 502 through 523 removed outlier: 5.393A pdb=" N ASP F 511 " --> pdb=" O GLU F 507 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR F 512 " --> pdb=" O GLN F 508 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 532 Processing helix chain 'F' and resid 571 through 584 removed outlier: 3.529A pdb=" N PHE F 575 " --> pdb=" O CYS F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 611 removed outlier: 3.645A pdb=" N VAL F 590 " --> pdb=" O PRO F 586 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU F 611 " --> pdb=" O SER F 607 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 646 removed outlier: 3.689A pdb=" N LYS F 646 " --> pdb=" O ALA F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 666 Processing helix chain 'H' and resid 427 through 435 Processing helix chain 'H' and resid 465 through 472 Processing helix chain 'H' and resid 489 through 518 removed outlier: 3.516A pdb=" N ASN H 518 " --> pdb=" O ASP H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 522 through 557 removed outlier: 3.611A pdb=" N ARG H 526 " --> pdb=" O THR H 522 " (cutoff:3.500A) Proline residue: H 540 - end of helix removed outlier: 3.588A pdb=" N ASN H 557 " --> pdb=" O GLU H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 564 Processing helix chain 'H' and resid 575 through 658 removed outlier: 3.780A pdb=" N ALA H 579 " --> pdb=" O ASN H 575 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA H 635 " --> pdb=" O HIS H 631 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN H 657 " --> pdb=" O LYS H 653 " (cutoff:3.500A) Processing helix chain 'I' and resid 678 through 693 removed outlier: 3.596A pdb=" N ILE I 682 " --> pdb=" O ASP I 678 " (cutoff:3.500A) Processing helix chain 'I' and resid 698 through 702 Processing helix chain 'I' and resid 707 through 716 Processing helix chain 'I' and resid 718 through 734 Processing helix chain 'I' and resid 746 through 765 removed outlier: 3.959A pdb=" N ASP I 750 " --> pdb=" O PRO I 746 " (cutoff:3.500A) Processing helix chain 'I' and resid 791 through 809 Processing helix chain 'I' and resid 883 through 896 Processing helix chain 'I' and resid 909 through 929 Processing helix chain 'I' and resid 931 through 941 removed outlier: 3.926A pdb=" N ARG I 940 " --> pdb=" O ARG I 936 " (cutoff:3.500A) Processing helix chain 'I' and resid 941 through 957 removed outlier: 3.683A pdb=" N LYS I 945 " --> pdb=" O ASN I 941 " (cutoff:3.500A) Processing helix chain 'I' and resid 958 through 962 removed outlier: 4.351A pdb=" N ASN I 961 " --> pdb=" O HIS I 958 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE I 962 " --> pdb=" O PRO I 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 958 through 962' Processing helix chain 'I' and resid 964 through 983 removed outlier: 3.660A pdb=" N ILE I 968 " --> pdb=" O CYS I 964 " (cutoff:3.500A) Processing helix chain 'I' and resid 990 through 1003 removed outlier: 3.764A pdb=" N CYS I 994 " --> pdb=" O SER I 990 " (cutoff:3.500A) Processing helix chain 'I' and resid 1035 through 1047 removed outlier: 3.742A pdb=" N GLY I1039 " --> pdb=" O TYR I1035 " (cutoff:3.500A) Processing helix chain 'I' and resid 1051 through 1063 Processing helix chain 'I' and resid 1078 through 1094 Processing helix chain 'I' and resid 1103 through 1116 Processing helix chain 'I' and resid 1118 through 1125 removed outlier: 3.810A pdb=" N GLN I1125 " --> pdb=" O GLN I1121 " (cutoff:3.500A) Processing helix chain 'I' and resid 1130 through 1154 Proline residue: I1138 - end of helix Processing helix chain 'I' and resid 1188 through 1195 Processing helix chain 'I' and resid 1199 through 1214 removed outlier: 3.510A pdb=" N GLY I1203 " --> pdb=" O ASN I1199 " (cutoff:3.500A) Processing helix chain 'I' and resid 1233 through 1260 removed outlier: 3.694A pdb=" N ILE I1239 " --> pdb=" O PRO I1235 " (cutoff:3.500A) Processing helix chain 'I' and resid 1264 through 1271 removed outlier: 3.638A pdb=" N LYS I1268 " --> pdb=" O GLU I1264 " (cutoff:3.500A) Processing helix chain 'I' and resid 1278 through 1288 removed outlier: 3.519A pdb=" N ILE I1282 " --> pdb=" O THR I1278 " (cutoff:3.500A) Processing helix chain 'I' and resid 1292 through 1314 Processing helix chain 'J' and resid 3 through 10 Processing helix chain 'K' and resid 52 through 53 No H-bonds generated for 'chain 'K' and resid 52 through 53' Processing helix chain 'K' and resid 55 through 55 No H-bonds generated for 'chain 'K' and resid 55 through 55' Processing helix chain 'K' and resid 56 through 60 Processing helix chain 'K' and resid 79 through 84 Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 115 through 116 No H-bonds generated for 'chain 'K' and resid 115 through 116' Processing helix chain 'K' and resid 118 through 118 No H-bonds generated for 'chain 'K' and resid 118 through 118' Processing helix chain 'K' and resid 119 through 128 Processing helix chain 'K' and resid 140 through 148 Processing helix chain 'K' and resid 176 through 179 Processing helix chain 'K' and resid 185 through 198 Processing helix chain 'K' and resid 199 through 201 No H-bonds generated for 'chain 'K' and resid 199 through 201' Processing helix chain 'K' and resid 216 through 226 Processing helix chain 'K' and resid 226 through 234 Processing helix chain 'K' and resid 242 through 262 removed outlier: 3.719A pdb=" N ILE K 256 " --> pdb=" O GLU K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 285 Processing helix chain 'K' and resid 293 through 296 Processing helix chain 'K' and resid 303 through 315 removed outlier: 4.013A pdb=" N PHE K 309 " --> pdb=" O GLU K 305 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA K 310 " --> pdb=" O CYS K 306 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR K 312 " --> pdb=" O GLN K 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU K 313 " --> pdb=" O PHE K 309 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE K 314 " --> pdb=" O ALA K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 316 through 319 Processing helix chain 'K' and resid 324 through 328 Processing helix chain 'K' and resid 331 through 332 No H-bonds generated for 'chain 'K' and resid 331 through 332' Processing helix chain 'K' and resid 334 through 334 No H-bonds generated for 'chain 'K' and resid 334 through 334' Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 381 through 389 removed outlier: 4.341A pdb=" N SER K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 401 Processing helix chain 'K' and resid 406 through 416 removed outlier: 3.792A pdb=" N ARG K 415 " --> pdb=" O GLU K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 442 Processing helix chain 'K' and resid 448 through 452 removed outlier: 3.941A pdb=" N GLY K 452 " --> pdb=" O TRP K 449 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 464 Processing helix chain 'L' and resid 5 through 8 Processing helix chain 'L' and resid 57 through 61 removed outlier: 3.591A pdb=" N ASN L 60 " --> pdb=" O ASN L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 99 Processing helix chain 'L' and resid 120 through 134 Processing helix chain 'L' and resid 145 through 152 Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.529A pdb=" N ASN L 195 " --> pdb=" O GLY L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 Processing helix chain 'L' and resid 275 through 279 Processing helix chain 'L' and resid 295 through 300 Processing helix chain 'L' and resid 302 through 318 Processing helix chain 'L' and resid 322 through 330 removed outlier: 3.646A pdb=" N ALA L 328 " --> pdb=" O ASN L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 337 through 342 Processing helix chain 'L' and resid 344 through 358 Processing helix chain 'L' and resid 362 through 373 Processing helix chain 'L' and resid 416 through 423 Processing helix chain 'L' and resid 427 through 441 Processing helix chain 'L' and resid 451 through 455 Processing helix chain 'L' and resid 457 through 465 removed outlier: 3.524A pdb=" N ALA L 460 " --> pdb=" O LYS L 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283 removed outlier: 4.330A pdb=" N LEU A 438 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 439 " --> pdb=" O HIS C 207 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 removed outlier: 3.641A pdb=" N SER A 184 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 Processing sheet with id=AA5, first strand: chain 'B' and resid 781 through 784 Processing sheet with id=AA6, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA7, first strand: chain 'D' and resid 319 through 320 removed outlier: 4.096A pdb=" N ILE D 319 " --> pdb=" O TYR I 778 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 312 through 313 Processing sheet with id=AA9, first strand: chain 'F' and resid 424 through 427 Processing sheet with id=AB1, first strand: chain 'F' and resid 457 through 464 Processing sheet with id=AB2, first strand: chain 'F' and resid 734 through 735 Processing sheet with id=AB3, first strand: chain 'H' and resid 425 through 426 removed outlier: 6.391A pdb=" N VAL H 425 " --> pdb=" O PHE H 453 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER H 452 " --> pdb=" O TYR I 664 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS H 439 " --> pdb=" O VAL I 661 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASN I 663 " --> pdb=" O LYS H 439 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL H 441 " --> pdb=" O ASN I 663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 478 through 479 Processing sheet with id=AB5, first strand: chain 'J' and resid 25 through 30 Processing sheet with id=AB6, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.407A pdb=" N VAL K 8 " --> pdb=" O VAL K 105 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU K 104 " --> pdb=" O GLN K 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 47 through 48 Processing sheet with id=AB8, first strand: chain 'K' and resid 173 through 174 Processing sheet with id=AB9, first strand: chain 'K' and resid 173 through 174 removed outlier: 6.311A pdb=" N VAL K 392 " --> pdb=" O PHE K 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 287 through 292 Processing sheet with id=AC2, first strand: chain 'L' and resid 35 through 38 removed outlier: 3.659A pdb=" N LEU L 35 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU L 10 " --> pdb=" O LEU L 112 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE L 114 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE L 12 " --> pdb=" O ILE L 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'L' and resid 68 through 69 Processing sheet with id=AC5, first strand: chain 'L' and resid 178 through 179 Processing sheet with id=AC6, first strand: chain 'L' and resid 178 through 179 Processing sheet with id=AC7, first strand: chain 'L' and resid 282 through 285 1573 hydrogen bonds defined for protein. 4500 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: 5.55 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5959 1.33 - 1.45: 6853 1.45 - 1.57: 17394 1.57 - 1.69: 1 1.69 - 1.81: 126 Bond restraints: 30333 Sorted by residual: bond pdb=" C SER K 380 " pdb=" N PRO K 381 " ideal model delta sigma weight residual 1.335 1.404 -0.069 1.30e-02 5.92e+03 2.79e+01 bond pdb=" N PRO K 381 " pdb=" CD PRO K 381 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.43e+01 bond pdb=" N LEU A 416 " pdb=" CA LEU A 416 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.80e+01 bond pdb=" CA ALA L 326 " pdb=" CB ALA L 326 " ideal model delta sigma weight residual 1.530 1.468 0.061 1.56e-02 4.11e+03 1.55e+01 bond pdb=" N PHE I1276 " pdb=" CA PHE I1276 " ideal model delta sigma weight residual 1.453 1.487 -0.033 9.20e-03 1.18e+04 1.32e+01 ... (remaining 30328 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 40348 3.17 - 6.33: 576 6.33 - 9.50: 26 9.50 - 12.67: 4 12.67 - 15.84: 2 Bond angle restraints: 40956 Sorted by residual: angle pdb=" N ARG F 468 " pdb=" CA ARG F 468 " pdb=" C ARG F 468 " ideal model delta sigma weight residual 108.49 100.91 7.58 1.15e+00 7.56e-01 4.34e+01 angle pdb=" C THR F 357 " pdb=" N ASN F 358 " pdb=" CA ASN F 358 " ideal model delta sigma weight residual 121.54 134.02 -12.48 1.91e+00 2.74e-01 4.27e+01 angle pdb=" C SER K 380 " pdb=" N PRO K 381 " pdb=" CA PRO K 381 " ideal model delta sigma weight residual 118.97 113.10 5.87 1.04e+00 9.25e-01 3.19e+01 angle pdb=" C PHE I1028 " pdb=" N GLN I1029 " pdb=" CA GLN I1029 " ideal model delta sigma weight residual 121.54 132.27 -10.73 1.91e+00 2.74e-01 3.16e+01 angle pdb=" N LYS K 176 " pdb=" CA LYS K 176 " pdb=" C LYS K 176 " ideal model delta sigma weight residual 111.28 117.21 -5.93 1.09e+00 8.42e-01 2.96e+01 ... (remaining 40951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16361 18.00 - 36.00: 1664 36.00 - 54.00: 428 54.00 - 72.00: 110 72.00 - 90.00: 35 Dihedral angle restraints: 18598 sinusoidal: 7782 harmonic: 10816 Sorted by residual: dihedral pdb=" CA ASP F 469 " pdb=" C ASP F 469 " pdb=" N ARG F 470 " pdb=" CA ARG F 470 " ideal model delta harmonic sigma weight residual -180.00 -151.16 -28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ILE A 61 " pdb=" C ILE A 61 " pdb=" N PRO A 62 " pdb=" CA PRO A 62 " ideal model delta harmonic sigma weight residual 180.00 -151.54 -28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ILE F 633 " pdb=" C ILE F 633 " pdb=" N THR F 634 " pdb=" CA THR F 634 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 18595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 4240 0.112 - 0.224: 322 0.224 - 0.337: 27 0.337 - 0.449: 2 0.449 - 0.561: 2 Chirality restraints: 4593 Sorted by residual: chirality pdb=" CA PHE L 447 " pdb=" N PHE L 447 " pdb=" C PHE L 447 " pdb=" CB PHE L 447 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB VAL E 207 " pdb=" CA VAL E 207 " pdb=" CG1 VAL E 207 " pdb=" CG2 VAL E 207 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CA ILE L 359 " pdb=" N ILE L 359 " pdb=" C ILE L 359 " pdb=" CB ILE L 359 " both_signs ideal model delta sigma weight residual False 2.43 2.86 -0.42 2.00e-01 2.50e+01 4.46e+00 ... (remaining 4590 not shown) Planarity restraints: 5233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 177 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C GLU C 177 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU C 177 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 178 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 866 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" C GLU I 866 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU I 866 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO I 867 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 550 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO E 551 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 551 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 551 " -0.033 5.00e-02 4.00e+02 ... (remaining 5230 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3196 2.74 - 3.28: 29022 3.28 - 3.82: 47192 3.82 - 4.36: 57646 4.36 - 4.90: 98618 Nonbonded interactions: 235674 Sorted by model distance: nonbonded pdb=" OE2 GLU F 574 " pdb=" OG1 THR I 790 " model vdw 2.196 3.040 nonbonded pdb=" NZ LYS D 461 " pdb=" OD2 ASP D 465 " model vdw 2.204 3.120 nonbonded pdb=" NH2 ARG B 380 " pdb=" OD1 ASN F 570 " model vdw 2.205 3.120 nonbonded pdb=" OG SER D 311 " pdb=" O TRP D 388 " model vdw 2.211 3.040 nonbonded pdb=" O GLU D 642 " pdb=" OG SER D 645 " model vdw 2.212 3.040 ... (remaining 235669 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 299 through 742 or resid 762 through 781)) selection = (chain 'D' and (resid 299 through 468 or resid 514 through 640 or resid 666 thro \ ugh 742 or resid 762 through 781)) } 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=0.36 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.640 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.008 0.069 30334 Z= 0.409 Angle : 0.961 15.836 40959 Z= 0.608 Chirality : 0.062 0.561 4593 Planarity : 0.005 0.059 5232 Dihedral : 16.234 89.999 11517 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.79 % Favored : 93.43 % Rotamer: Outliers : 6.35 % Allowed : 14.56 % Favored : 79.10 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3490 helix: -0.38 (0.11), residues: 1888 sheet: -0.46 (0.33), residues: 232 loop : -2.14 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 420 TYR 0.025 0.002 TYR L 454 PHE 0.019 0.002 PHE L 447 TRP 0.015 0.003 TRP L 419 HIS 0.009 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00770 (30333) covalent geometry : angle 0.96079 (40956) hydrogen bonds : bond 0.15588 ( 1569) hydrogen bonds : angle 6.11095 ( 4500) link_TRANS : bond 0.00318 ( 1) link_TRANS : angle 0.92708 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 246 time to evaluate : 1.240 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 156 TRP cc_start: 0.6797 (t60) cc_final: 0.6434 (t60) REVERT: A 403 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7169 (tp) REVERT: A 443 GLU cc_start: 0.8281 (pp20) cc_final: 0.7989 (pp20) REVERT: C 165 THR cc_start: 0.8695 (m) cc_final: 0.8494 (p) REVERT: D 522 GLN cc_start: 0.8294 (mm110) cc_final: 0.7787 (tp40) REVERT: D 589 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8219 (pt) REVERT: D 770 PHE cc_start: 0.7367 (m-10) cc_final: 0.7160 (m-10) REVERT: E 123 MET cc_start: 0.8023 (ptt) cc_final: 0.7498 (tmm) REVERT: E 318 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7664 (p90) REVERT: I 932 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7316 (t0) REVERT: I 1106 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8997 (tt) REVERT: K 262 GLU cc_start: 0.1440 (OUTLIER) cc_final: 0.0940 (pt0) REVERT: K 397 SER cc_start: -0.0674 (OUTLIER) cc_final: -0.1063 (t) REVERT: L 34 GLU cc_start: 0.1441 (OUTLIER) cc_final: 0.0397 (mt-10) outliers start: 212 outliers final: 85 residues processed: 441 average time/residue: 0.6721 time to fit residues: 348.4745 Evaluate side-chains 227 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 134 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 526 ASN Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 643 GLU Chi-restraints excluded: chain D residue 657 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 406 SER Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain H residue 447 ASP Chi-restraints excluded: chain H residue 459 SER Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain H residue 558 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 713 SER Chi-restraints excluded: chain I residue 736 SER Chi-restraints excluded: chain I residue 741 SER Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 808 THR Chi-restraints excluded: chain I residue 867 PRO Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 932 ASP Chi-restraints excluded: chain I residue 939 SER Chi-restraints excluded: chain I residue 980 SER Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1115 SER Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1143 SER Chi-restraints excluded: chain I residue 1192 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 90 ARG Chi-restraints excluded: chain K residue 122 ARG Chi-restraints excluded: chain K residue 262 GLU Chi-restraints excluded: chain K residue 397 SER Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 54 HIS Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 438 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 95 HIS A 153 ASN A 171 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 556 ASN A 563 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 522 GLN B 533 GLN B 738 ASN B 766 GLN C 200 GLN D 303 HIS D 359 ASN D 394 GLN D 416 HIS D 522 GLN D 587 ASN D 640 GLN D 678 GLN D 680 ASN D 690 GLN E 204 GLN E 298 HIS E 317 GLN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 473 HIS F 434 ASN F 556 GLN F 614 ASN H 462 ASN H 564 HIS H 589 HIS I 718 ASN I 765 GLN I 805 ASN I 915 ASN I 970 ASN I 981 ASN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN I1100 ASN I1120 GLN I1284 GLN I1300 GLN K 214 GLN K 230 GLN L 116 HIS B L 167 HIS L 303 ASN L 304 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.149944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096381 restraints weight = 86025.234| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.62 r_work: 0.3033 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30334 Z= 0.152 Angle : 0.622 14.795 40959 Z= 0.324 Chirality : 0.043 0.175 4593 Planarity : 0.005 0.055 5232 Dihedral : 7.357 95.686 4054 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.85 % Favored : 94.81 % Rotamer: Outliers : 4.07 % Allowed : 17.16 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3490 helix: 1.41 (0.12), residues: 1904 sheet: -0.26 (0.31), residues: 257 loop : -1.70 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 465 TYR 0.026 0.002 TYR K 455 PHE 0.016 0.001 PHE J 87 TRP 0.015 0.001 TRP L 463 HIS 0.016 0.001 HIS L 167 Details of bonding type rmsd covalent geometry : bond 0.00339 (30333) covalent geometry : angle 0.62240 (40956) hydrogen bonds : bond 0.05988 ( 1569) hydrogen bonds : angle 4.32441 ( 4500) link_TRANS : bond 0.00204 ( 1) link_TRANS : angle 0.92386 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 166 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8993 (tt) REVERT: B 303 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7434 (m-70) REVERT: B 638 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7886 (ttpt) REVERT: B 711 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: C 165 THR cc_start: 0.8689 (m) cc_final: 0.8474 (p) REVERT: D 450 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (pt0) REVERT: D 522 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8002 (tp40) REVERT: D 589 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8291 (pt) REVERT: E 123 MET cc_start: 0.8274 (ptt) cc_final: 0.7518 (tmm) REVERT: E 206 ILE cc_start: 0.8561 (mp) cc_final: 0.8310 (mp) REVERT: F 629 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8818 (mpt) REVERT: F 653 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8492 (mt) REVERT: H 434 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.6700 (t80) REVERT: I 667 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8702 (mp) REVERT: G 118 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6540 (ppt170) REVERT: K 204 GLU cc_start: 0.1679 (OUTLIER) cc_final: 0.1433 (mp0) REVERT: K 262 GLU cc_start: 0.1753 (OUTLIER) cc_final: 0.1514 (pt0) REVERT: L 293 LYS cc_start: 0.0953 (mttp) cc_final: 0.0635 (pmtt) outliers start: 136 outliers final: 45 residues processed: 284 average time/residue: 0.5964 time to fit residues: 204.3850 Evaluate side-chains 195 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 137 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 303 HIS Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 711 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 587 ASN Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 622 THR Chi-restraints excluded: chain D residue 653 ILE Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 749 VAL Chi-restraints excluded: chain H residue 429 VAL Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain I residue 665 LYS Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1106 LEU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain K residue 204 GLU Chi-restraints excluded: chain K residue 262 GLU Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 82 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 0.2980 chunk 295 optimal weight: 9.9990 chunk 282 optimal weight: 0.0170 chunk 146 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 301 GLN B 522 GLN C 231 HIS D 394 GLN D 587 ASN ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 554 GLN H 562 ASN ** I1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1036 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.151726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092975 restraints weight = 68489.427| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.11 r_work: 0.3157 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30334 Z= 0.118 Angle : 0.554 13.900 40959 Z= 0.285 Chirality : 0.041 0.187 4593 Planarity : 0.004 0.048 5232 Dihedral : 5.959 85.684 3965 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.53 % Favored : 95.21 % Rotamer: Outliers : 3.44 % Allowed : 17.85 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.14), residues: 3490 helix: 2.10 (0.12), residues: 1916 sheet: 0.13 (0.33), residues: 249 loop : -1.43 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 248 TYR 0.021 0.001 TYR K 257 PHE 0.025 0.001 PHE H 629 TRP 0.027 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00240 (30333) covalent geometry : angle 0.55370 (40956) hydrogen bonds : bond 0.04836 ( 1569) hydrogen bonds : angle 3.96661 ( 4500) link_TRANS : bond 0.00275 ( 1) link_TRANS : angle 1.03954 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 175 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 GLU cc_start: 0.8264 (pt0) cc_final: 0.7935 (pt0) REVERT: B 462 ARG cc_start: 0.7984 (tmm160) cc_final: 0.7514 (tmm-80) REVERT: B 638 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7859 (ttpt) REVERT: C 240 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6724 (t80) REVERT: D 374 ASP cc_start: 0.8832 (p0) cc_final: 0.8404 (p0) REVERT: D 450 GLU cc_start: 0.8071 (pt0) cc_final: 0.7808 (pt0) REVERT: D 522 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8105 (tp40) REVERT: D 589 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8190 (pt) REVERT: E 123 MET cc_start: 0.8195 (ptt) cc_final: 0.7365 (tpp) REVERT: E 327 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8046 (m110) REVERT: F 621 GLU cc_start: 0.8363 (tt0) cc_final: 0.7985 (pp20) REVERT: F 629 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8870 (mpt) REVERT: F 653 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8426 (mt) REVERT: H 434 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6825 (t80) REVERT: H 460 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5674 (m90) REVERT: I 667 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8754 (mp) REVERT: G 118 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6778 (ppt170) REVERT: K 455 TYR cc_start: 0.5372 (OUTLIER) cc_final: 0.5067 (t80) REVERT: L 293 LYS cc_start: 0.1251 (mttp) cc_final: 0.0924 (pmtt) outliers start: 115 outliers final: 45 residues processed: 274 average time/residue: 0.6017 time to fit residues: 198.2437 Evaluate side-chains 203 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 147 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 775 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain F residue 743 VAL Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain I residue 667 LEU Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1124 SER Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 358 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 266 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 344 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN C 231 HIS D 394 GLN D 587 ASN E 38 HIS H 562 ASN I1006 GLN K 79 ASN K 286 GLN A L 438 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.151623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.098608 restraints weight = 91902.180| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.86 r_work: 0.3054 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30334 Z= 0.118 Angle : 0.547 14.286 40959 Z= 0.279 Chirality : 0.041 0.183 4593 Planarity : 0.004 0.049 5232 Dihedral : 5.583 93.231 3948 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 3.11 % Allowed : 18.93 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.15), residues: 3490 helix: 2.36 (0.12), residues: 1909 sheet: 0.39 (0.33), residues: 254 loop : -1.35 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.018 0.001 TYR D 576 PHE 0.015 0.001 PHE H 629 TRP 0.032 0.001 TRP A 156 HIS 0.015 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00255 (30333) covalent geometry : angle 0.54710 (40956) hydrogen bonds : bond 0.04801 ( 1569) hydrogen bonds : angle 3.81971 ( 4500) link_TRANS : bond 0.00213 ( 1) link_TRANS : angle 0.87999 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 148 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7139 (ttt) REVERT: B 638 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7890 (ttpt) REVERT: B 763 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.6275 (mp) REVERT: C 240 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6748 (t80) REVERT: D 374 ASP cc_start: 0.8798 (p0) cc_final: 0.8372 (p0) REVERT: D 450 GLU cc_start: 0.8070 (pt0) cc_final: 0.7831 (pt0) REVERT: D 522 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8131 (tp40) REVERT: D 589 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8152 (pt) REVERT: E 123 MET cc_start: 0.8244 (ptt) cc_final: 0.7374 (tpp) REVERT: E 327 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.7793 (p0) REVERT: E 331 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: F 621 GLU cc_start: 0.8254 (tt0) cc_final: 0.8009 (pp20) REVERT: F 629 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8812 (mpt) REVERT: F 653 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8466 (mt) REVERT: H 434 TYR cc_start: 0.7611 (OUTLIER) cc_final: 0.6919 (t80) REVERT: G 118 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6754 (ppt170) REVERT: K 455 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5335 (t80) outliers start: 104 outliers final: 47 residues processed: 238 average time/residue: 0.5808 time to fit residues: 168.1389 Evaluate side-chains 191 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 132 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 763 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 469 ASP Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 638 VAL Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 358 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 259 optimal weight: 5.9990 chunk 322 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 191 optimal weight: 0.4980 chunk 342 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN D 567 GLN F 448 GLN I1243 GLN I1284 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.151198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093575 restraints weight = 81298.982| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.40 r_work: 0.3139 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 30334 Z= 0.110 Angle : 0.525 13.736 40959 Z= 0.268 Chirality : 0.040 0.192 4593 Planarity : 0.004 0.053 5232 Dihedral : 5.306 84.220 3944 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.35 % Rotamer: Outliers : 2.96 % Allowed : 18.93 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3490 helix: 2.53 (0.12), residues: 1917 sheet: 0.54 (0.34), residues: 252 loop : -1.22 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 465 TYR 0.018 0.001 TYR D 576 PHE 0.018 0.001 PHE H 629 TRP 0.024 0.001 TRP A 156 HIS 0.006 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00231 (30333) covalent geometry : angle 0.52497 (40956) hydrogen bonds : bond 0.04449 ( 1569) hydrogen bonds : angle 3.69328 ( 4500) link_TRANS : bond 0.00241 ( 1) link_TRANS : angle 0.94349 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 163 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 147 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8121 (tt0) REVERT: C 151 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7212 (mp0) REVERT: C 240 TYR cc_start: 0.7704 (OUTLIER) cc_final: 0.7052 (t80) REVERT: D 374 ASP cc_start: 0.8871 (p0) cc_final: 0.8435 (p0) REVERT: D 450 GLU cc_start: 0.8075 (pt0) cc_final: 0.7869 (pt0) REVERT: D 522 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8238 (tp-100) REVERT: D 589 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8154 (pt) REVERT: E 123 MET cc_start: 0.8177 (ptt) cc_final: 0.7385 (tpp) REVERT: E 327 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8338 (OUTLIER) REVERT: F 621 GLU cc_start: 0.8449 (tt0) cc_final: 0.8157 (pp20) REVERT: F 629 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8903 (mpt) REVERT: F 653 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8477 (mt) REVERT: H 434 TYR cc_start: 0.7607 (OUTLIER) cc_final: 0.6868 (t80) REVERT: H 460 HIS cc_start: 0.6383 (OUTLIER) cc_final: 0.5960 (m90) REVERT: I 1198 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: G 118 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6891 (ppt170) REVERT: K 455 TYR cc_start: 0.5716 (OUTLIER) cc_final: 0.5406 (t80) outliers start: 99 outliers final: 51 residues processed: 247 average time/residue: 0.5665 time to fit residues: 169.5802 Evaluate side-chains 195 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 603 MET Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 486 VAL Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1198 GLU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 455 TYR Chi-restraints excluded: chain L residue 323 ILE Chi-restraints excluded: chain L residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 45 optimal weight: 1.9990 chunk 344 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 228 optimal weight: 0.9990 chunk 287 optimal weight: 0.0470 chunk 219 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN K 63 ASN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.149570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087694 restraints weight = 91281.432| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.82 r_work: 0.3075 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30334 Z= 0.136 Angle : 0.551 14.387 40959 Z= 0.280 Chirality : 0.041 0.191 4593 Planarity : 0.004 0.055 5232 Dihedral : 5.107 51.312 3939 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.56 % Favored : 95.21 % Rotamer: Outliers : 2.88 % Allowed : 19.05 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 3490 helix: 2.54 (0.12), residues: 1916 sheet: 0.66 (0.34), residues: 253 loop : -1.16 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 465 TYR 0.018 0.001 TYR D 576 PHE 0.015 0.001 PHE K 244 TRP 0.019 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00310 (30333) covalent geometry : angle 0.55088 (40956) hydrogen bonds : bond 0.04917 ( 1569) hydrogen bonds : angle 3.71486 ( 4500) link_TRANS : bond 0.00165 ( 1) link_TRANS : angle 0.79191 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 146 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 638 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7938 (ttpt) REVERT: C 240 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 241 HIS cc_start: 0.4789 (OUTLIER) cc_final: 0.4531 (t-90) REVERT: D 522 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8255 (tp-100) REVERT: D 589 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8254 (pt) REVERT: E 123 MET cc_start: 0.8313 (ptt) cc_final: 0.7469 (tpp) REVERT: E 327 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8318 (OUTLIER) REVERT: F 424 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8179 (m) REVERT: F 468 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6464 (mtm-85) REVERT: F 629 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8852 (mpt) REVERT: H 434 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6848 (t80) REVERT: H 460 HIS cc_start: 0.6421 (OUTLIER) cc_final: 0.6014 (m90) REVERT: G 118 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6844 (ppt170) outliers start: 96 outliers final: 52 residues processed: 228 average time/residue: 0.5847 time to fit residues: 160.8696 Evaluate side-chains 202 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1050 GLU Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain I residue 1311 THR Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 221 optimal weight: 30.0000 chunk 312 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 354 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN D 394 GLN F 448 GLN I 675 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.149238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087870 restraints weight = 84309.607| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.66 r_work: 0.3082 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30334 Z= 0.141 Angle : 0.554 14.897 40959 Z= 0.282 Chirality : 0.041 0.210 4593 Planarity : 0.004 0.055 5232 Dihedral : 5.125 52.035 3938 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.62 % Favored : 95.09 % Rotamer: Outliers : 2.79 % Allowed : 19.29 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.15), residues: 3490 helix: 2.52 (0.12), residues: 1921 sheet: 0.72 (0.34), residues: 251 loop : -1.13 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 462 TYR 0.050 0.001 TYR K 455 PHE 0.016 0.001 PHE K 244 TRP 0.017 0.001 TRP A 156 HIS 0.010 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00326 (30333) covalent geometry : angle 0.55389 (40956) hydrogen bonds : bond 0.05000 ( 1569) hydrogen bonds : angle 3.72450 ( 4500) link_TRANS : bond 0.00160 ( 1) link_TRANS : angle 0.82412 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 142 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 638 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7909 (ttpt) REVERT: C 240 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7036 (t80) REVERT: C 241 HIS cc_start: 0.4904 (OUTLIER) cc_final: 0.4623 (t-90) REVERT: D 450 GLU cc_start: 0.7816 (pt0) cc_final: 0.7441 (pt0) REVERT: D 522 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8238 (tp40) REVERT: D 589 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8270 (pt) REVERT: E 123 MET cc_start: 0.8254 (ptt) cc_final: 0.7475 (tpp) REVERT: E 327 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8341 (p0) REVERT: F 424 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8267 (m) REVERT: F 468 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6530 (mtm-85) REVERT: F 629 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8828 (mpt) REVERT: H 434 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6895 (t80) REVERT: H 460 HIS cc_start: 0.6271 (OUTLIER) cc_final: 0.5804 (m90) REVERT: H 517 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (mp) REVERT: I 659 SER cc_start: 0.6338 (OUTLIER) cc_final: 0.5655 (p) REVERT: I 1308 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8501 (t0) REVERT: G 118 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6857 (ppt170) outliers start: 93 outliers final: 59 residues processed: 222 average time/residue: 0.5761 time to fit residues: 154.8079 Evaluate side-chains 211 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 638 LYS Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 517 LEU Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 903 ASN Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1131 LEU Chi-restraints excluded: chain I residue 1214 ILE Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain I residue 1308 ASP Chi-restraints excluded: chain I residue 1311 THR Chi-restraints excluded: chain G residue 118 ARG Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 90 ARG Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 215 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 171 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 328 optimal weight: 30.0000 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 0.0870 chunk 8 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 GLN D 394 GLN F 448 GLN H 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.151868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094851 restraints weight = 96231.529| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.69 r_work: 0.3135 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30334 Z= 0.106 Angle : 0.526 13.693 40959 Z= 0.267 Chirality : 0.040 0.189 4593 Planarity : 0.004 0.054 5232 Dihedral : 4.911 53.496 3938 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.36 % Favored : 95.44 % Rotamer: Outliers : 2.43 % Allowed : 19.80 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.15), residues: 3490 helix: 2.72 (0.12), residues: 1928 sheet: 0.85 (0.35), residues: 251 loop : -1.08 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 462 TYR 0.024 0.001 TYR K 455 PHE 0.016 0.001 PHE K 244 TRP 0.016 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00216 (30333) covalent geometry : angle 0.52589 (40956) hydrogen bonds : bond 0.04183 ( 1569) hydrogen bonds : angle 3.59655 ( 4500) link_TRANS : bond 0.00279 ( 1) link_TRANS : angle 1.03036 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 156 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 240 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7008 (t80) REVERT: C 241 HIS cc_start: 0.4822 (OUTLIER) cc_final: 0.4443 (t-90) REVERT: D 374 ASP cc_start: 0.8670 (p0) cc_final: 0.8368 (p0) REVERT: D 522 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8109 (tp-100) REVERT: D 589 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8095 (pt) REVERT: E 123 MET cc_start: 0.8125 (ptt) cc_final: 0.7276 (tpp) REVERT: E 327 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8346 (OUTLIER) REVERT: F 468 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6391 (mtt180) REVERT: F 629 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8804 (mpt) REVERT: H 434 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6916 (t80) REVERT: I 659 SER cc_start: 0.5984 (OUTLIER) cc_final: 0.5376 (p) outliers start: 81 outliers final: 44 residues processed: 224 average time/residue: 0.5860 time to fit residues: 158.6793 Evaluate side-chains 189 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 321 optimal weight: 0.1980 chunk 180 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 285 optimal weight: 30.0000 chunk 354 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 282 optimal weight: 50.0000 chunk 137 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN H 562 ASN L 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.150619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092516 restraints weight = 92159.415| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.21 r_work: 0.3073 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30334 Z= 0.114 Angle : 0.535 13.980 40959 Z= 0.272 Chirality : 0.040 0.183 4593 Planarity : 0.004 0.056 5232 Dihedral : 4.794 54.408 3932 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 2.34 % Allowed : 19.83 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.15), residues: 3490 helix: 2.75 (0.12), residues: 1922 sheet: 0.88 (0.35), residues: 251 loop : -0.99 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 462 TYR 0.017 0.001 TYR D 576 PHE 0.016 0.001 PHE K 244 TRP 0.015 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00248 (30333) covalent geometry : angle 0.53542 (40956) hydrogen bonds : bond 0.04367 ( 1569) hydrogen bonds : angle 3.58813 ( 4500) link_TRANS : bond 0.00219 ( 1) link_TRANS : angle 0.85635 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 145 time to evaluate : 1.330 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: C 240 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6979 (t80) REVERT: C 241 HIS cc_start: 0.4911 (OUTLIER) cc_final: 0.4459 (t-90) REVERT: D 374 ASP cc_start: 0.8755 (p0) cc_final: 0.8429 (p0) REVERT: D 450 GLU cc_start: 0.7127 (pt0) cc_final: 0.6797 (pt0) REVERT: D 522 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8078 (tp40) REVERT: D 589 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8088 (pt) REVERT: E 123 MET cc_start: 0.8243 (ptt) cc_final: 0.7286 (tpp) REVERT: E 327 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8360 (OUTLIER) REVERT: F 629 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8788 (mpt) REVERT: F 739 MET cc_start: 0.9466 (mmm) cc_final: 0.9259 (tpp) REVERT: H 434 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.6931 (t80) REVERT: H 460 HIS cc_start: 0.6083 (OUTLIER) cc_final: 0.5714 (m90) REVERT: I 659 SER cc_start: 0.6109 (OUTLIER) cc_final: 0.5471 (p) outliers start: 78 outliers final: 53 residues processed: 213 average time/residue: 0.5581 time to fit residues: 144.0584 Evaluate side-chains 196 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain E residue 519 TYR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain H residue 434 TYR Chi-restraints excluded: chain H residue 460 HIS Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 790 THR Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 90 ARG Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 323 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 36 optimal weight: 0.9980 chunk 320 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 356 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 328 optimal weight: 40.0000 chunk 38 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN I1142 GLN L 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.151063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098124 restraints weight = 102986.526| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.04 r_work: 0.3054 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30334 Z= 0.109 Angle : 0.530 13.751 40959 Z= 0.268 Chirality : 0.040 0.180 4593 Planarity : 0.004 0.058 5232 Dihedral : 4.728 55.450 3932 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.62 % Favored : 95.15 % Rotamer: Outliers : 1.98 % Allowed : 20.22 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.15), residues: 3490 helix: 2.79 (0.12), residues: 1930 sheet: 0.94 (0.34), residues: 251 loop : -0.98 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 462 TYR 0.018 0.001 TYR D 576 PHE 0.016 0.001 PHE K 244 TRP 0.013 0.001 TRP A 156 HIS 0.006 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00232 (30333) covalent geometry : angle 0.53035 (40956) hydrogen bonds : bond 0.04208 ( 1569) hydrogen bonds : angle 3.54587 ( 4500) link_TRANS : bond 0.00231 ( 1) link_TRANS : angle 0.90716 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6980 Ramachandran restraints generated. 3490 Oldfield, 0 Emsley, 3490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 143 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 240 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 241 HIS cc_start: 0.5041 (OUTLIER) cc_final: 0.4577 (t-90) REVERT: D 374 ASP cc_start: 0.8803 (p0) cc_final: 0.8497 (p0) REVERT: D 450 GLU cc_start: 0.7159 (pt0) cc_final: 0.6838 (pt0) REVERT: D 522 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8115 (tp40) REVERT: D 589 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8159 (pt) REVERT: E 123 MET cc_start: 0.8216 (ptt) cc_final: 0.7297 (tpp) REVERT: E 327 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8383 (OUTLIER) REVERT: F 629 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8894 (mpt) REVERT: F 653 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8235 (mt) REVERT: I 659 SER cc_start: 0.6080 (OUTLIER) cc_final: 0.5475 (p) REVERT: I 1198 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: L 47 GLN cc_start: 0.0906 (OUTLIER) cc_final: 0.0692 (tm-30) outliers start: 66 outliers final: 45 residues processed: 200 average time/residue: 0.5648 time to fit residues: 137.9067 Evaluate side-chains 187 residues out of total 3337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 196 HIS Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 391 ILE Chi-restraints excluded: chain D residue 394 GLN Chi-restraints excluded: chain D residue 420 ARG Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 589 LEU Chi-restraints excluded: chain D residue 779 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 357 THR Chi-restraints excluded: chain F residue 360 TYR Chi-restraints excluded: chain F residue 424 THR Chi-restraints excluded: chain F residue 432 VAL Chi-restraints excluded: chain F residue 578 SER Chi-restraints excluded: chain F residue 616 ASP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain H residue 478 THR Chi-restraints excluded: chain H residue 522 THR Chi-restraints excluded: chain I residue 659 SER Chi-restraints excluded: chain I residue 679 ILE Chi-restraints excluded: chain I residue 698 PHE Chi-restraints excluded: chain I residue 768 VAL Chi-restraints excluded: chain I residue 1085 LEU Chi-restraints excluded: chain I residue 1198 GLU Chi-restraints excluded: chain I residue 1232 VAL Chi-restraints excluded: chain I residue 1236 SER Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 325 optimal weight: 8.9990 chunk 119 optimal weight: 0.0050 chunk 67 optimal weight: 2.9990 chunk 116 optimal weight: 0.0170 chunk 280 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 overall best weight: 0.7834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN F 448 GLN L 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.150901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.088699 restraints weight = 76630.130| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.51 r_work: 0.3105 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30334 Z= 0.112 Angle : 0.534 13.946 40959 Z= 0.270 Chirality : 0.040 0.319 4593 Planarity : 0.004 0.057 5232 Dihedral : 4.683 55.961 3929 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 1.77 % Allowed : 20.58 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.15), residues: 3490 helix: 2.81 (0.12), residues: 1928 sheet: 0.97 (0.34), residues: 251 loop : -0.97 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 425 TYR 0.017 0.001 TYR D 576 PHE 0.016 0.001 PHE K 244 TRP 0.013 0.001 TRP A 156 HIS 0.007 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00244 (30333) covalent geometry : angle 0.53407 (40956) hydrogen bonds : bond 0.04255 ( 1569) hydrogen bonds : angle 3.53713 ( 4500) link_TRANS : bond 0.00217 ( 1) link_TRANS : angle 0.87462 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16830.38 seconds wall clock time: 285 minutes 39.79 seconds (17139.79 seconds total)