Starting phenix.real_space_refine on Sat Jan 18 21:38:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w0e_43707/01_2025/8w0e_43707_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w0e_43707/01_2025/8w0e_43707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w0e_43707/01_2025/8w0e_43707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w0e_43707/01_2025/8w0e_43707.map" model { file = "/net/cci-nas-00/data/ceres_data/8w0e_43707/01_2025/8w0e_43707_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w0e_43707/01_2025/8w0e_43707_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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: 8 Type Number sf(0) Gaussians Zn 5 6.06 5 P 61 5.49 5 Mg 5 5.21 5 S 172 5.16 5 C 18712 2.51 5 N 5319 2.21 5 O 5808 1.98 5 H 29690 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 59772 Number of models: 1 Model: "" Number of chains: 14 Chain: "2" Number of atoms: 10277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 10277 Classifications: {'peptide': 649} Link IDs: {'PTRANS': 28, 'TRANS': 620} Chain breaks: 2 Chain: "3" Number of atoms: 9618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 9618 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 4 Chain: "4" Number of atoms: 10085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 10085 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 29, 'TRANS': 599} Chain breaks: 2 Chain: "5" Number of atoms: 9315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 9315 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 5 Chain: "6" Number of atoms: 9455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9455 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 21, 'TRANS': 568} Chain breaks: 4 Chain: "7" Number of atoms: 9271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9271 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain breaks: 7 Chain: "O" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 801 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "S" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 801 Classifications: {'DNA': 25} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 24} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2506 SG CYS 2 329 34.052 82.713 98.553 1.00172.04 S ATOM 2552 SG CYS 2 332 30.310 82.997 99.037 1.00171.93 S ATOM 2844 SG CYS 2 352 32.354 85.653 100.474 1.00170.30 S ATOM 2883 SG CYS 2 355 32.536 82.452 102.177 1.00183.14 S ATOM 22581 SG CYS 4 306 71.371 102.199 116.945 1.00153.93 S ATOM 22624 SG CYS 4 309 73.285 104.743 118.952 1.00156.45 S ATOM 22913 SG CYS 4 328 73.435 101.135 119.978 1.00153.94 S ATOM 22954 SG CYS 4 331 70.129 103.018 120.380 1.00161.60 S ATOM 32279 SG CYS 5 172 39.798 63.464 106.378 1.00180.09 S ATOM 32324 SG CYS 5 175 37.286 62.907 107.397 1.00183.30 S ATOM 32675 SG CYS 5 197 36.161 65.563 107.108 1.00167.88 S ATOM 41651 SG CYS 6 158 55.428 96.801 110.449 1.00232.75 S ATOM 41692 SG CYS 6 161 54.523 98.726 113.007 1.00228.96 S ATOM 42010 SG CYS 6 180 57.660 98.812 112.877 1.00230.11 S ATOM 51548 SG CYS 7 184 79.461 75.327 123.902 1.00160.55 S ATOM 51587 SG CYS 7 187 79.815 72.592 126.310 1.00162.26 S ATOM 51876 SG CYS 7 206 76.567 72.742 124.282 1.00160.22 S ATOM 51943 SG CYS 7 211 77.193 75.242 127.042 1.00188.23 S Time building chain proxies: 23.98, per 1000 atoms: 0.40 Number of scatterers: 59772 At special positions: 0 Unit cell: (147.264, 143.104, 142.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 5 29.99 S 172 16.00 P 61 15.00 Mg 5 11.99 O 5808 8.00 N 5319 7.00 C 18712 6.00 H 29690 1.00 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 Atom "HETATM59679 O3A ADP 31002 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21000 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21000 " - pdb=" SG CYS 2 355 " pdb=" ZN 41000 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 41000 " - pdb=" SG CYS 4 331 " pdb=" ZN 51000 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 197 " pdb="ZN ZN 51000 " - pdb=" SG CYS 5 175 " pdb=" ZN 61000 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 61000 " - pdb=" SG CYS 6 180 " pdb=" ZN 71000 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 184 " pdb="ZN ZN 71000 " - pdb=" SG CYS 7 206 " Number of angles added : 18 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6928 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 41 sheets defined 45.8% alpha, 18.3% beta 25 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 23.80 Creating SS restraints... Processing helix chain '2' and resid 181 through 188 Processing helix chain '2' and resid 188 through 206 Processing helix chain '2' and resid 213 through 226 removed outlier: 3.705A pdb=" N GLU 2 217 " --> pdb=" O ASN 2 213 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 241 Processing helix chain '2' and resid 241 through 251 Proline residue: 2 249 - end of helix Processing helix chain '2' and resid 251 through 271 removed outlier: 3.502A pdb=" N GLU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 277 Processing helix chain '2' and resid 293 through 297 removed outlier: 3.588A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 459 through 469 removed outlier: 3.667A pdb=" N MET 2 463 " --> pdb=" O GLU 2 459 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS 2 469 " --> pdb=" O THR 2 465 " (cutoff:3.500A) Processing helix chain '2' and resid 472 through 480 Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 528 through 540 Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 593 through 607 Processing helix chain '2' and resid 632 through 636 removed outlier: 4.132A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) Processing helix chain '2' and resid 642 through 646 Processing helix chain '2' and resid 650 through 655 Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 716 through 730 Processing helix chain '2' and resid 739 through 757 Processing helix chain '2' and resid 763 through 782 removed outlier: 3.718A pdb=" N ILE 2 767 " --> pdb=" O THR 2 763 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 805 Processing helix chain '2' and resid 807 through 818 Processing helix chain '2' and resid 818 through 823 Processing helix chain '2' and resid 827 through 849 removed outlier: 3.687A pdb=" N LEU 2 831 " --> pdb=" O ASP 2 827 " (cutoff:3.500A) Processing helix chain '3' and resid 10 through 24 Processing helix chain '3' and resid 30 through 42 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 58 through 68 Processing helix chain '3' and resid 68 through 88 removed outlier: 3.710A pdb=" N GLU 3 72 " --> pdb=" O ASN 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 95 removed outlier: 3.610A pdb=" N GLN 3 94 " --> pdb=" O THR 3 90 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR 3 95 " --> pdb=" O TYR 3 91 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 269 through 273 Processing helix chain '3' and resid 278 through 291 removed outlier: 4.303A pdb=" N ARG 3 291 " --> pdb=" O PHE 3 287 " (cutoff:3.500A) Processing helix chain '3' and resid 294 through 302 Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 362 Processing helix chain '3' and resid 374 through 378 Processing helix chain '3' and resid 398 through 402 Processing helix chain '3' and resid 410 through 414 Processing helix chain '3' and resid 415 through 421 Processing helix chain '3' and resid 422 through 428 Processing helix chain '3' and resid 464 through 469 Processing helix chain '3' and resid 472 through 479 Processing helix chain '3' and resid 490 through 507 Processing helix chain '3' and resid 549 through 554 Processing helix chain '3' and resid 564 through 577 removed outlier: 3.945A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 583 through 599 Processing helix chain '3' and resid 600 through 603 Processing helix chain '3' and resid 614 through 632 removed outlier: 3.639A pdb=" N LEU 3 618 " --> pdb=" O THR 3 614 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG 3 632 " --> pdb=" O HIS 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 653 removed outlier: 3.501A pdb=" N ALA 3 642 " --> pdb=" O ASP 3 638 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 172 Processing helix chain '4' and resid 191 through 204 Processing helix chain '4' and resid 212 through 219 Processing helix chain '4' and resid 219 through 229 Processing helix chain '4' and resid 229 through 248 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 270 through 274 Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 431 through 437 Processing helix chain '4' and resid 442 through 455 removed outlier: 3.614A pdb=" N LYS 4 455 " --> pdb=" O GLU 4 451 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 466 removed outlier: 3.678A pdb=" N LEU 4 466 " --> pdb=" O LEU 4 462 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 516 through 525 Processing helix chain '4' and resid 534 through 538 Processing helix chain '4' and resid 539 through 544 Processing helix chain '4' and resid 561 through 566 removed outlier: 3.537A pdb=" N SER 4 566 " --> pdb=" O ALA 4 562 " (cutoff:3.500A) Processing helix chain '4' and resid 580 through 593 removed outlier: 4.067A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU 4 587 " --> pdb=" O THR 4 583 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS 4 588 " --> pdb=" O ARG 4 584 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU 4 589 " --> pdb=" O SER 4 585 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL 4 590 " --> pdb=" O VAL 4 586 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 623 removed outlier: 4.202A pdb=" N GLN 4 623 " --> pdb=" O ILE 4 620 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 644 removed outlier: 3.554A pdb=" N PHE 4 644 " --> pdb=" O LEU 4 640 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 672 Processing helix chain '4' and resid 683 through 698 removed outlier: 3.805A pdb=" N ASP 4 689 " --> pdb=" O ALA 4 685 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 721 Processing helix chain '4' and resid 730 through 748 removed outlier: 3.765A pdb=" N LEU 4 734 " --> pdb=" O TYR 4 730 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 768 Processing helix chain '4' and resid 769 through 771 No H-bonds generated for 'chain '4' and resid 769 through 771' Processing helix chain '5' and resid 28 through 42 Processing helix chain '5' and resid 53 through 66 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 81 through 91 removed outlier: 3.564A pdb=" N ALA 5 85 " --> pdb=" O ASP 5 81 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 112 removed outlier: 3.525A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 Processing helix chain '5' and resid 216 through 219 removed outlier: 3.567A pdb=" N CYS 5 219 " --> pdb=" O PRO 5 216 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 216 through 219' Processing helix chain '5' and resid 315 through 328 removed outlier: 3.531A pdb=" N LEU 5 328 " --> pdb=" O ARG 5 324 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 337 Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 387 through 398 Processing helix chain '5' and resid 432 through 437 Processing helix chain '5' and resid 451 through 465 removed outlier: 4.308A pdb=" N GLU 5 463 " --> pdb=" O HIS 5 459 " (cutoff:3.500A) Processing helix chain '5' and resid 496 through 500 Processing helix chain '5' and resid 507 through 514 removed outlier: 3.601A pdb=" N ARG 5 513 " --> pdb=" O THR 5 509 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE 5 514 " --> pdb=" O ILE 5 510 " (cutoff:3.500A) Processing helix chain '5' and resid 526 through 543 Processing helix chain '5' and resid 555 through 570 Processing helix chain '5' and resid 575 through 601 Processing helix chain '5' and resid 609 through 627 removed outlier: 3.916A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 652 removed outlier: 3.610A pdb=" N SER 5 647 " --> pdb=" O LEU 5 643 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP 5 650 " --> pdb=" O VAL 5 646 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 37 Processing helix chain '6' and resid 44 through 52 removed outlier: 3.936A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 55 No H-bonds generated for 'chain '6' and resid 53 through 55' Processing helix chain '6' and resid 65 through 72 Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 100 Proline residue: 6 88 - end of helix Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 127 through 131 Processing helix chain '6' and resid 321 through 329 Processing helix chain '6' and resid 330 through 342 Processing helix chain '6' and resid 345 through 355 Processing helix chain '6' and resid 361 through 374 Processing helix chain '6' and resid 401 through 413 Processing helix chain '6' and resid 425 through 430 Processing helix chain '6' and resid 447 through 452 Processing helix chain '6' and resid 462 through 465 Processing helix chain '6' and resid 466 through 480 removed outlier: 4.230A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) Processing helix chain '6' and resid 505 through 509 removed outlier: 3.997A pdb=" N HIS 6 509 " --> pdb=" O ILE 6 506 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 520 removed outlier: 3.583A pdb=" N ILE 6 520 " --> pdb=" O LEU 6 516 " (cutoff:3.500A) Processing helix chain '6' and resid 523 through 529 removed outlier: 3.625A pdb=" N ARG 6 529 " --> pdb=" O PRO 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 558 Processing helix chain '6' and resid 568 through 580 Processing helix chain '6' and resid 587 through 605 removed outlier: 3.989A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 3.715A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS 6 635 " --> pdb=" O MET 6 631 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 3.566A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 19 Processing helix chain '7' and resid 31 through 42 removed outlier: 3.743A pdb=" N GLN 7 36 " --> pdb=" O LYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 59 removed outlier: 4.033A pdb=" N ASP 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 59 through 69 Processing helix chain '7' and resid 70 through 85 Processing helix chain '7' and resid 86 through 88 No H-bonds generated for 'chain '7' and resid 86 through 88' Processing helix chain '7' and resid 97 through 110 Processing helix chain '7' and resid 127 through 131 Processing helix chain '7' and resid 148 through 152 Processing helix chain '7' and resid 153 through 157 Processing helix chain '7' and resid 208 through 215 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 307 through 310 Processing helix chain '7' and resid 324 through 328 Processing helix chain '7' and resid 331 through 339 Processing helix chain '7' and resid 347 through 360 removed outlier: 3.587A pdb=" N LEU 7 356 " --> pdb=" O LYS 7 352 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 396 Processing helix chain '7' and resid 410 through 414 Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 447 through 450 Processing helix chain '7' and resid 451 through 465 Processing helix chain '7' and resid 509 through 513 Processing helix chain '7' and resid 526 through 544 Processing helix chain '7' and resid 555 through 568 removed outlier: 3.579A pdb=" N ARG 7 561 " --> pdb=" O LYS 7 557 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU 7 568 " --> pdb=" O ALA 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 595 removed outlier: 4.325A pdb=" N ASP 7 579 " --> pdb=" O GLU 7 575 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR 7 580 " --> pdb=" O SER 7 576 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 7 587 " --> pdb=" O ALA 7 583 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA 7 592 " --> pdb=" O MET 7 588 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 621 removed outlier: 3.922A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 645 removed outlier: 3.576A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU 7 644 " --> pdb=" O SER 7 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 Processing sheet with id=AA2, first strand: chain '2' and resid 339 through 340 removed outlier: 3.620A pdb=" N VAL 2 325 " --> pdb=" O PHE 2 339 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE 2 369 " --> pdb=" O SER 2 323 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ALA 2 441 " --> pdb=" O ASP 2 395 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE 2 397 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N HIS 2 443 " --> pdb=" O ILE 2 397 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 443 " (cutoff:3.500A) removed outlier: 13.577A pdb=" N ALA 2 445 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS 2 446 " --> pdb=" O GLU 2 411 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU 2 411 " --> pdb=" O LYS 2 446 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 543 through 547 removed outlier: 6.626A pdb=" N ILE 2 544 " --> pdb=" O LEU 2 585 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP 2 587 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU 2 520 " --> pdb=" O CYS 2 661 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL 2 663 " --> pdb=" O LEU 2 520 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N CYS 2 522 " --> pdb=" O VAL 2 663 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 559 through 562 Processing sheet with id=AA5, first strand: chain '2' and resid 608 through 611 Processing sheet with id=AA6, first strand: chain '3' and resid 46 through 50 removed outlier: 6.262A pdb=" N LEU 3 47 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU 3 103 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL 3 49 " --> pdb=" O GLU 3 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '3' and resid 123 through 134 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 123 through 134 current: chain '3' and resid 154 through 158 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 154 through 158 current: chain '3' and resid 216 through 221 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 216 through 221 current: chain '3' and resid 255 through 267 removed outlier: 4.234A pdb=" N ALA 5 163 " --> pdb=" O PHE 3 256 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 5 168 " --> pdb=" O ILE 5 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 251 through 252 Processing sheet with id=AA9, first strand: chain '3' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain '3' and resid 365 through 368 removed outlier: 6.700A pdb=" N GLY 3 404 " --> pdb=" O SER 3 447 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU 3 449 " --> pdb=" O GLY 3 404 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ALA 3 452 " --> pdb=" O ILE 3 341 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU 3 343 " --> pdb=" O ALA 3 452 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 3 342 " --> pdb=" O PHE 3 483 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N MET 3 485 " --> pdb=" O LEU 3 342 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE 3 344 " --> pdb=" O MET 3 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 381 through 384 Processing sheet with id=AB3, first strand: chain '3' and resid 430 through 435 Processing sheet with id=AB4, first strand: chain '3' and resid 581 through 582 removed outlier: 6.670A pdb=" N VAL 3 581 " --> pdb=" O VAL 3 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '3' and resid 607 through 609 Processing sheet with id=AB6, first strand: chain '4' and resid 207 through 211 removed outlier: 6.587A pdb=" N LEU 4 208 " --> pdb=" O ARG 4 261 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE 4 263 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL 4 210 " --> pdb=" O PHE 4 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '4' and resid 312 through 316 removed outlier: 7.635A pdb=" N PHE 4 346 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N MET 4 299 " --> pdb=" O SER 4 344 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N SER 4 344 " --> pdb=" O MET 4 299 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N GLU 4 301 " --> pdb=" O ASN 4 342 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASN 4 342 " --> pdb=" O GLU 4 301 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE 4 303 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N THR 4 369 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N ILE 4 416 " --> pdb=" O THR 4 369 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE 4 371 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 371 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE 4 373 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N HIS 4 420 " --> pdb=" O PHE 4 373 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS 4 375 " --> pdb=" O HIS 4 420 " (cutoff:3.500A) removed outlier: 13.921A pdb=" N ARG 4 422 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR 4 421 " --> pdb=" O ASN 4 389 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN 4 389 " --> pdb=" O TYR 4 421 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR 4 292 " --> pdb=" O MET 4 351 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET 4 351 " --> pdb=" O THR 4 292 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 408 through 409 removed outlier: 3.734A pdb=" N VAL 4 408 " --> pdb=" O PHE 7 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 531 through 533 removed outlier: 6.644A pdb=" N GLN 4 531 " --> pdb=" O CYS 4 572 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS 4 571 " --> pdb=" O LEU 4 614 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA 4 616 " --> pdb=" O CYS 4 571 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE 4 573 " --> pdb=" O ALA 4 616 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 545 through 549 Processing sheet with id=AC2, first strand: chain '4' and resid 595 through 599 Processing sheet with id=AC3, first strand: chain '4' and resid 701 through 702 removed outlier: 6.512A pdb=" N ARG 4 701 " --> pdb=" O VAL 4 753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain '5' and resid 69 through 73 Processing sheet with id=AC5, first strand: chain '5' and resid 148 through 158 removed outlier: 6.536A pdb=" N LYS 5 228 " --> pdb=" O ILE 5 156 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ALA 5 158 " --> pdb=" O THR 5 226 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR 5 226 " --> pdb=" O ALA 5 158 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N HIS 5 244 " --> pdb=" O SER 5 292 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE 5 294 " --> pdb=" O HIS 5 244 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN 5 246 " --> pdb=" O ILE 5 294 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL 5 296 " --> pdb=" O GLN 5 246 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR 5 248 " --> pdb=" O VAL 5 296 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLY 5 298 " --> pdb=" O TYR 5 248 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET 5 266 " --> pdb=" O LEU 5 297 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE 5 299 " --> pdb=" O THR 5 264 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR 5 264 " --> pdb=" O ILE 5 299 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL 5 301 " --> pdb=" O ARG 5 262 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG 5 262 " --> pdb=" O VAL 5 301 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 170 through 172 Processing sheet with id=AC7, first strand: chain '5' and resid 363 through 364 Processing sheet with id=AC8, first strand: chain '5' and resid 401 through 405 removed outlier: 6.735A pdb=" N VAL 5 402 " --> pdb=" O CYS 5 443 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP 5 445 " --> pdb=" O VAL 5 402 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR 5 404 " --> pdb=" O ASP 5 445 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU 5 377 " --> pdb=" O ALA 5 486 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ALA 5 488 " --> pdb=" O LEU 5 377 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N MET 5 379 " --> pdb=" O ALA 5 488 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 417 through 420 Processing sheet with id=AD1, first strand: chain '5' and resid 466 through 470 Processing sheet with id=AD2, first strand: chain '5' and resid 573 through 574 removed outlier: 6.947A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '6' and resid 60 through 64 Processing sheet with id=AD4, first strand: chain '6' and resid 164 through 169 removed outlier: 5.895A pdb=" N GLY 6 154 " --> pdb=" O ASP 6 167 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU 6 169 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL 6 152 " --> pdb=" O GLU 6 169 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL 6 152 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU 6 225 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE 6 298 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG 6 229 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N CYS 6 302 " --> pdb=" O ARG 6 229 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU 6 296 " --> pdb=" O VAL 6 251 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL 6 251 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE 6 298 " --> pdb=" O ILE 6 249 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE 6 249 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA 6 300 " --> pdb=" O THR 6 247 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR 6 247 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '6' and resid 378 through 379 Processing sheet with id=AD6, first strand: chain '6' and resid 416 through 419 removed outlier: 6.631A pdb=" N GLY 6 455 " --> pdb=" O SER 6 498 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU 6 500 " --> pdb=" O GLY 6 455 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY 6 396 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '6' and resid 431 through 435 Processing sheet with id=AD8, first strand: chain '6' and resid 481 through 486 Processing sheet with id=AD9, first strand: chain '6' and resid 585 through 586 removed outlier: 7.151A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '7' and resid 47 through 51 Processing sheet with id=AE2, first strand: chain '7' and resid 190 through 194 removed outlier: 7.323A pdb=" N PHE 7 229 " --> pdb=" O PRO 7 175 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N MET 7 177 " --> pdb=" O SER 7 227 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N SER 7 227 " --> pdb=" O MET 7 177 " (cutoff:3.500A) removed outlier: 10.701A pdb=" N VAL 7 179 " --> pdb=" O ARG 7 225 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ARG 7 225 " --> pdb=" O VAL 7 179 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR 7 254 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU 7 258 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ARG 7 302 " --> pdb=" O GLU 7 258 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU 7 295 " --> pdb=" O ILE 7 280 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR 7 274 " --> pdb=" O HIS 7 301 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE 7 303 " --> pdb=" O SER 7 272 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER 7 272 " --> pdb=" O ILE 7 303 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS 7 305 " --> pdb=" O HIS 7 270 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N HIS 7 270 " --> pdb=" O LYS 7 305 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS 7 236 " --> pdb=" O THR 7 168 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL 7 170 " --> pdb=" O GLU 7 234 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU 7 234 " --> pdb=" O VAL 7 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '7' and resid 401 through 405 removed outlier: 6.158A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP 7 445 " --> pdb=" O GLN 7 402 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR 7 404 " --> pdb=" O ASP 7 445 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N CYS 7 442 " --> pdb=" O LEU 7 485 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA 7 487 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE 7 444 " --> pdb=" O ALA 7 487 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N CYS 7 378 " --> pdb=" O TRP 7 519 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE 7 521 " --> pdb=" O CYS 7 378 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET 7 380 " --> pdb=" O ILE 7 521 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '7' and resid 417 through 419 Processing sheet with id=AE5, first strand: chain '7' and resid 466 through 469 removed outlier: 3.523A pdb=" N ILE 7 469 " --> pdb=" O THR 7 476 " (cutoff:3.500A) 1290 hydrogen bonds defined for protein. 3657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 24.73 Time building geometry restraints manager: 15.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 29637 1.03 - 1.23: 87 1.23 - 1.42: 12509 1.42 - 1.62: 17859 1.62 - 1.81: 273 Bond restraints: 60365 Sorted by residual: bond pdb=" C ARG 4 272 " pdb=" O ARG 4 272 " ideal model delta sigma weight residual 1.236 1.206 0.031 1.24e-02 6.50e+03 6.07e+00 bond pdb=" C ASN 7 631 " pdb=" O ASN 7 631 " ideal model delta sigma weight residual 1.236 1.219 0.017 1.15e-02 7.56e+03 2.30e+00 bond pdb=" NE2 HIS 7 536 " pdb=" HE2 HIS 7 536 " ideal model delta sigma weight residual 0.860 0.834 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" CA MET 4 650 " pdb=" C MET 4 650 " ideal model delta sigma weight residual 1.524 1.509 0.014 1.27e-02 6.20e+03 1.29e+00 bond pdb=" CE1 TYR 5 42 " pdb=" CZ TYR 5 42 " ideal model delta sigma weight residual 1.378 1.352 0.026 2.40e-02 1.74e+03 1.15e+00 ... (remaining 60360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 106653 1.40 - 2.79: 2357 2.79 - 4.19: 211 4.19 - 5.58: 33 5.58 - 6.98: 7 Bond angle restraints: 109261 Sorted by residual: angle pdb=" N VAL 3 142 " pdb=" CA VAL 3 142 " pdb=" C VAL 3 142 " ideal model delta sigma weight residual 113.71 109.68 4.03 9.50e-01 1.11e+00 1.80e+01 angle pdb=" N ILE 7 264 " pdb=" CA ILE 7 264 " pdb=" C ILE 7 264 " ideal model delta sigma weight residual 112.96 109.48 3.48 1.00e+00 1.00e+00 1.21e+01 angle pdb=" C HIS 7 347 " pdb=" CA HIS 7 347 " pdb=" CB HIS 7 347 " ideal model delta sigma weight residual 111.51 106.02 5.49 1.58e+00 4.01e-01 1.21e+01 angle pdb=" N GLY 2 179 " pdb=" CA GLY 2 179 " pdb=" C GLY 2 179 " ideal model delta sigma weight residual 111.21 114.79 -3.58 1.04e+00 9.25e-01 1.19e+01 angle pdb=" C ILE 2 277 " pdb=" N THR 2 278 " pdb=" CA THR 2 278 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 ... (remaining 109256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.07: 27115 34.07 - 68.14: 921 68.14 - 102.21: 30 102.21 - 136.27: 4 136.27 - 170.34: 1 Dihedral angle restraints: 28071 sinusoidal: 15998 harmonic: 12073 Sorted by residual: dihedral pdb=" O1B ADP 71002 " pdb=" O3A ADP 71002 " pdb=" PB ADP 71002 " pdb=" PA ADP 71002 " ideal model delta sinusoidal sigma weight residual -60.00 110.34 -170.34 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP 51002 " pdb=" O3A ADP 51002 " pdb=" PA ADP 51002 " pdb=" PB ADP 51002 " ideal model delta sinusoidal sigma weight residual -60.00 64.75 -124.75 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" C5' ADP 51002 " pdb=" O5' ADP 51002 " pdb=" PA ADP 51002 " pdb=" O2A ADP 51002 " ideal model delta sinusoidal sigma weight residual 300.00 177.87 122.13 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 28068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3000 0.029 - 0.057: 1082 0.057 - 0.086: 321 0.086 - 0.115: 242 0.115 - 0.144: 72 Chirality restraints: 4717 Sorted by residual: chirality pdb=" CA ILE 2 760 " pdb=" N ILE 2 760 " pdb=" C ILE 2 760 " pdb=" CB ILE 2 760 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE 3 484 " pdb=" N ILE 3 484 " pdb=" C ILE 3 484 " pdb=" CB ILE 3 484 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE 4 174 " pdb=" N ILE 4 174 " pdb=" C ILE 4 174 " pdb=" CB ILE 4 174 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 4714 not shown) Planarity restraints: 8697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET 4 194 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C MET 4 194 " 0.026 2.00e-02 2.50e+03 pdb=" O MET 4 194 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN 4 195 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY 5 571 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO 5 572 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO 5 572 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO 5 572 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE 5 393 " 0.018 2.00e-02 2.50e+03 8.64e-03 2.24e+00 pdb=" CG PHE 5 393 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE 5 393 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 5 393 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE 5 393 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 5 393 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 5 393 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE 5 393 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE 5 393 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE 5 393 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE 5 393 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE 5 393 " 0.001 2.00e-02 2.50e+03 ... (remaining 8694 not shown) Histogram of nonbonded interaction distances: 1.34 - 1.99: 541 1.99 - 2.65: 81772 2.65 - 3.30: 182534 3.30 - 3.95: 231960 3.95 - 4.60: 362263 Nonbonded interactions: 859070 Sorted by model distance: nonbonded pdb=" O GLU 7 343 " pdb=" HE2 HIS 7 536 " model vdw 1.343 2.450 nonbonded pdb=" OD1 ASN 5 525 " pdb=" H ARG 5 528 " model vdw 1.519 2.450 nonbonded pdb=" H LEU 3 244 " pdb=" O ARG 3 257 " model vdw 1.536 2.450 nonbonded pdb=" O VAL 7 167 " pdb=" H GLY 7 268 " model vdw 1.551 2.450 nonbonded pdb=" HD1 HIS 2 777 " pdb=" OD1 ASP 2 790 " model vdw 1.573 2.450 ... (remaining 859065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.780 Extract box with map and model: 1.970 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 145.710 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.200 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: 0.040 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.002 0.034 30675 Z= 0.152 Angle : 0.535 6.975 41628 Z= 0.291 Chirality : 0.040 0.144 4717 Planarity : 0.003 0.037 5203 Dihedral : 14.574 170.343 11920 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.63 % Allowed : 8.38 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3587 helix: 1.31 (0.14), residues: 1413 sheet: -1.02 (0.20), residues: 665 loop : -0.70 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 334 HIS 0.004 0.001 HIS 5 95 PHE 0.024 0.001 PHE 5 393 TYR 0.011 0.001 TYR 2 535 ARG 0.003 0.000 ARG 5 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 361 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 341 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 746 MET cc_start: 0.8657 (tmm) cc_final: 0.8277 (tmm) REVERT: 2 750 LEU cc_start: 0.9448 (mt) cc_final: 0.9235 (mt) REVERT: 2 753 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8380 (tm-30) REVERT: 3 38 GLU cc_start: 0.9523 (tp30) cc_final: 0.9014 (tp30) REVERT: 3 42 ASP cc_start: 0.8646 (p0) cc_final: 0.8314 (p0) REVERT: 4 294 GLN cc_start: 0.8649 (pt0) cc_final: 0.8426 (pm20) REVERT: 4 684 MET cc_start: 0.8752 (tpp) cc_final: 0.8378 (tpp) REVERT: 6 291 ASP cc_start: 0.8496 (m-30) cc_final: 0.7818 (p0) REVERT: 7 309 SER cc_start: 0.8918 (m) cc_final: 0.8623 (p) outliers start: 20 outliers final: 11 residues processed: 355 average time/residue: 0.8635 time to fit residues: 489.1702 Evaluate side-chains 298 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 287 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 689 SER Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 290 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 516 LYS Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 537 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 286 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 332 optimal weight: 0.3980 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 35 ASN 7 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.106682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087551 restraints weight = 220590.071| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.38 r_work: 0.3305 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30675 Z= 0.305 Angle : 0.585 7.109 41628 Z= 0.312 Chirality : 0.042 0.155 4717 Planarity : 0.004 0.056 5203 Dihedral : 13.736 171.907 4685 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.10 % Allowed : 10.19 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3587 helix: 1.28 (0.14), residues: 1450 sheet: -1.09 (0.20), residues: 675 loop : -0.87 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 334 HIS 0.007 0.001 HIS 7 459 PHE 0.027 0.001 PHE 5 393 TYR 0.017 0.001 TYR 2 535 ARG 0.006 0.000 ARG 3 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8202 (mmp) REVERT: 2 572 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7580 (mm-30) REVERT: 2 746 MET cc_start: 0.8506 (tmm) cc_final: 0.8158 (tmm) REVERT: 3 38 GLU cc_start: 0.9484 (tp30) cc_final: 0.8982 (tp30) REVERT: 3 42 ASP cc_start: 0.8651 (p0) cc_final: 0.8243 (p0) REVERT: 4 294 GLN cc_start: 0.8578 (pt0) cc_final: 0.8355 (pm20) REVERT: 6 291 ASP cc_start: 0.8780 (m-30) cc_final: 0.8140 (p0) REVERT: 6 466 ASP cc_start: 0.8775 (t70) cc_final: 0.8491 (t0) REVERT: 7 269 ASP cc_start: 0.8161 (m-30) cc_final: 0.7828 (m-30) outliers start: 35 outliers final: 19 residues processed: 320 average time/residue: 0.8187 time to fit residues: 420.5339 Evaluate side-chains 302 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 290 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 7 residue 99 LEU Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 520 LEU Chi-restraints excluded: chain 7 residue 537 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 75 optimal weight: 0.5980 chunk 267 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 171 GLN 7 35 ASN 7 238 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.106746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.088153 restraints weight = 216917.450| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.31 r_work: 0.3315 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30675 Z= 0.230 Angle : 0.545 7.406 41628 Z= 0.286 Chirality : 0.041 0.153 4717 Planarity : 0.004 0.048 5203 Dihedral : 13.624 172.676 4675 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.19 % Allowed : 10.82 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3587 helix: 1.42 (0.14), residues: 1452 sheet: -1.30 (0.20), residues: 661 loop : -0.84 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 334 HIS 0.004 0.001 HIS 5 95 PHE 0.025 0.001 PHE 5 393 TYR 0.014 0.001 TYR 2 535 ARG 0.006 0.000 ARG 3 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8166 (mmp) REVERT: 2 365 MET cc_start: 0.8618 (ptp) cc_final: 0.8259 (ptp) REVERT: 2 572 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7535 (mm-30) REVERT: 3 38 GLU cc_start: 0.9466 (tp30) cc_final: 0.9106 (tp30) REVERT: 3 133 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7234 (mttp) REVERT: 3 190 LEU cc_start: 0.9499 (mt) cc_final: 0.9230 (mp) REVERT: 3 391 ARG cc_start: 0.8541 (mmt90) cc_final: 0.8101 (mmt90) REVERT: 4 294 GLN cc_start: 0.8644 (pt0) cc_final: 0.8342 (pm20) REVERT: 6 517 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8079 (mttm) REVERT: 7 269 ASP cc_start: 0.8075 (m-30) cc_final: 0.7768 (m-30) outliers start: 38 outliers final: 32 residues processed: 326 average time/residue: 0.7917 time to fit residues: 412.5031 Evaluate side-chains 317 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 290 THR Chi-restraints excluded: chain 3 residue 475 LEU Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 272 LYS Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 99 LEU Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 537 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 15 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.106751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.088210 restraints weight = 216650.762| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.29 r_work: 0.3317 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30675 Z= 0.223 Angle : 0.537 6.870 41628 Z= 0.282 Chirality : 0.041 0.155 4717 Planarity : 0.003 0.045 5203 Dihedral : 13.559 169.767 4675 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.29 % Allowed : 11.07 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3587 helix: 1.50 (0.14), residues: 1448 sheet: -1.32 (0.20), residues: 654 loop : -0.83 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 4 624 HIS 0.004 0.001 HIS 5 540 PHE 0.025 0.001 PHE 5 393 TYR 0.015 0.001 TYR 2 535 ARG 0.005 0.000 ARG 2 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 296 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8161 (mmp) REVERT: 2 284 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6941 (mmt180) REVERT: 2 572 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7472 (mm-30) REVERT: 2 768 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8357 (mm-30) REVERT: 3 38 GLU cc_start: 0.9449 (tp30) cc_final: 0.9117 (tp30) REVERT: 3 133 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7476 (mttm) REVERT: 3 190 LEU cc_start: 0.9490 (mt) cc_final: 0.9211 (mp) REVERT: 3 391 ARG cc_start: 0.8522 (mmt90) cc_final: 0.8135 (mmt90) REVERT: 3 633 MET cc_start: 0.8891 (mmt) cc_final: 0.8633 (mmt) REVERT: 4 115 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7040 (ptp90) REVERT: 4 294 GLN cc_start: 0.8625 (pt0) cc_final: 0.8322 (pm20) REVERT: 6 517 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8064 (mttm) REVERT: 7 269 ASP cc_start: 0.8033 (m-30) cc_final: 0.7782 (m-30) REVERT: 7 588 MET cc_start: 0.8814 (mtp) cc_final: 0.8593 (mtp) outliers start: 41 outliers final: 30 residues processed: 323 average time/residue: 0.8606 time to fit residues: 446.5753 Evaluate side-chains 314 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 222 MET Chi-restraints excluded: chain 2 residue 284 ARG Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 822 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 290 THR Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 272 LYS Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 99 LEU Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 537 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 137 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 360 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.107049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088545 restraints weight = 216304.323| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.28 r_work: 0.3324 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30675 Z= 0.196 Angle : 0.529 6.503 41628 Z= 0.276 Chirality : 0.041 0.156 4717 Planarity : 0.003 0.043 5203 Dihedral : 13.453 166.555 4675 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.54 % Allowed : 11.70 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3587 helix: 1.58 (0.14), residues: 1449 sheet: -1.29 (0.20), residues: 654 loop : -0.82 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 334 HIS 0.004 0.001 HIS 5 540 PHE 0.024 0.001 PHE 5 393 TYR 0.014 0.001 TYR 2 535 ARG 0.006 0.000 ARG 2 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 352 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 284 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6872 (mmt180) REVERT: 2 572 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7403 (mm-30) REVERT: 2 811 MET cc_start: 0.9127 (ttp) cc_final: 0.8782 (ttm) REVERT: 3 38 GLU cc_start: 0.9445 (tp30) cc_final: 0.9137 (tp30) REVERT: 3 190 LEU cc_start: 0.9478 (mt) cc_final: 0.9196 (mp) REVERT: 3 391 ARG cc_start: 0.8494 (mmt90) cc_final: 0.8132 (mmt90) REVERT: 3 633 MET cc_start: 0.8875 (mmt) cc_final: 0.8578 (mmt) REVERT: 4 294 GLN cc_start: 0.8638 (pt0) cc_final: 0.8308 (pm20) REVERT: 4 543 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8819 (tp) REVERT: 5 129 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9235 (ptpp) REVERT: 7 269 ASP cc_start: 0.7965 (m-30) cc_final: 0.7727 (m-30) REVERT: 7 588 MET cc_start: 0.8849 (mtp) cc_final: 0.8610 (mtp) outliers start: 49 outliers final: 35 residues processed: 338 average time/residue: 0.8018 time to fit residues: 429.0488 Evaluate side-chains 322 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 284 ARG Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 497 LEU Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 2 residue 822 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 129 LYS Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 209 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 272 LYS Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 637 VAL Chi-restraints excluded: chain 6 residue 553 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 99 LEU Chi-restraints excluded: chain 7 residue 206 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 83 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 606 GLN 4 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.105139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086070 restraints weight = 222949.300| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.37 r_work: 0.3275 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30675 Z= 0.371 Angle : 0.591 7.071 41628 Z= 0.314 Chirality : 0.042 0.153 4717 Planarity : 0.004 0.086 5203 Dihedral : 13.490 165.584 4669 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.82 % Allowed : 12.55 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3587 helix: 1.36 (0.14), residues: 1448 sheet: -1.42 (0.20), residues: 623 loop : -0.96 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP 6 334 HIS 0.005 0.001 HIS 7 240 PHE 0.027 0.001 PHE 5 393 TYR 0.018 0.002 TYR 2 535 ARG 0.008 0.000 ARG 3 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 281 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8548 (mmp) cc_final: 0.8296 (mmp) REVERT: 2 284 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.6999 (mmt180) REVERT: 2 811 MET cc_start: 0.9167 (ttp) cc_final: 0.8815 (ttm) REVERT: 3 38 GLU cc_start: 0.9438 (tp30) cc_final: 0.9128 (tp30) REVERT: 4 162 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7960 (m) REVERT: 4 294 GLN cc_start: 0.8677 (pt0) cc_final: 0.8324 (pm20) REVERT: 4 543 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8807 (tp) REVERT: 5 129 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9223 (ptpp) REVERT: 7 269 ASP cc_start: 0.8173 (m-30) cc_final: 0.7787 (m-30) outliers start: 58 outliers final: 44 residues processed: 319 average time/residue: 0.8543 time to fit residues: 438.0451 Evaluate side-chains 322 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 274 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 284 ARG Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 605 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 735 LEU Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 2 residue 822 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 122 SER Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 290 THR Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 162 CYS Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 129 LYS Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 168 ILE Chi-restraints excluded: chain 5 residue 209 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 272 LYS Chi-restraints excluded: chain 5 residue 276 LEU Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 5 residue 626 MET Chi-restraints excluded: chain 6 residue 553 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 201 MET Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 234 GLU Chi-restraints excluded: chain 7 residue 554 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 203 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 606 GLN 6 556 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.106743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.088263 restraints weight = 216676.210| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.29 r_work: 0.3320 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30675 Z= 0.164 Angle : 0.529 6.727 41628 Z= 0.275 Chirality : 0.041 0.152 4717 Planarity : 0.003 0.088 5203 Dihedral : 13.338 160.543 4669 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.54 % Allowed : 12.77 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.14), residues: 3587 helix: 1.56 (0.14), residues: 1451 sheet: -1.40 (0.20), residues: 645 loop : -0.85 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 6 614 HIS 0.005 0.001 HIS 2 686 PHE 0.023 0.001 PHE 5 393 TYR 0.016 0.001 TYR 2 535 ARG 0.014 0.000 ARG 3 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 342 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 293 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8514 (mmp) cc_final: 0.8229 (mmp) REVERT: 2 284 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.6987 (mmt180) REVERT: 2 621 GLN cc_start: 0.7647 (pt0) cc_final: 0.7401 (pt0) REVERT: 2 811 MET cc_start: 0.9108 (ttp) cc_final: 0.8746 (ttm) REVERT: 3 38 GLU cc_start: 0.9447 (tp30) cc_final: 0.9165 (tp30) REVERT: 3 633 MET cc_start: 0.8872 (mmt) cc_final: 0.8603 (mmt) REVERT: 4 162 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7947 (m) REVERT: 4 294 GLN cc_start: 0.8654 (pt0) cc_final: 0.8316 (pm20) REVERT: 4 543 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8818 (tp) REVERT: 5 129 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9144 (ptpp) REVERT: 7 269 ASP cc_start: 0.7915 (m-30) cc_final: 0.7605 (m-30) outliers start: 49 outliers final: 37 residues processed: 326 average time/residue: 0.8114 time to fit residues: 424.3930 Evaluate side-chains 322 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 284 ARG Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 463 MET Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 605 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 735 LEU Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 2 residue 822 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 162 CYS Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 129 LYS Chi-restraints excluded: chain 5 residue 209 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 6 residue 493 LEU Chi-restraints excluded: chain 6 residue 553 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 276 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 34 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 306 optimal weight: 0.0270 chunk 74 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 324 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 overall best weight: 1.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 751 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.105946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087467 restraints weight = 217225.594| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.28 r_work: 0.3310 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30675 Z= 0.232 Angle : 0.539 6.794 41628 Z= 0.281 Chirality : 0.041 0.152 4717 Planarity : 0.004 0.096 5203 Dihedral : 13.288 156.014 4669 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.69 % Allowed : 12.74 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3587 helix: 1.59 (0.14), residues: 1447 sheet: -1.39 (0.20), residues: 642 loop : -0.84 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 6 334 HIS 0.004 0.001 HIS 5 540 PHE 0.025 0.001 PHE 5 393 TYR 0.016 0.001 TYR 2 535 ARG 0.016 0.000 ARG 3 257 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 3.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8478 (mmp) cc_final: 0.8208 (mmp) REVERT: 2 284 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.6998 (mmt180) REVERT: 2 572 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7397 (mm-30) REVERT: 2 621 GLN cc_start: 0.7790 (pt0) cc_final: 0.7518 (pt0) REVERT: 3 38 GLU cc_start: 0.9434 (tp30) cc_final: 0.9163 (tp30) REVERT: 3 633 MET cc_start: 0.8921 (mmt) cc_final: 0.8616 (mmt) REVERT: 4 162 CYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7938 (m) REVERT: 4 294 GLN cc_start: 0.8665 (pt0) cc_final: 0.8299 (pm20) REVERT: 4 543 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8815 (tp) REVERT: 5 129 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9143 (ptpp) REVERT: 7 269 ASP cc_start: 0.7963 (m-30) cc_final: 0.7638 (m-30) outliers start: 54 outliers final: 43 residues processed: 320 average time/residue: 0.8381 time to fit residues: 432.2627 Evaluate side-chains 324 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 284 ARG Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 463 MET Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 539 VAL Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 594 ASP Chi-restraints excluded: chain 2 residue 605 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 735 LEU Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 2 residue 822 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 122 SER Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 162 CYS Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 129 LYS Chi-restraints excluded: chain 5 residue 209 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 272 LYS Chi-restraints excluded: chain 5 residue 276 LEU Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 6 residue 553 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 206 CYS Chi-restraints excluded: chain 7 residue 234 GLU Chi-restraints excluded: chain 7 residue 276 ILE Chi-restraints excluded: chain 7 residue 404 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 253 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 324 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 347 optimal weight: 0.6980 chunk 287 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.106044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087641 restraints weight = 217321.908| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.26 r_work: 0.3312 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30675 Z= 0.231 Angle : 0.540 6.756 41628 Z= 0.282 Chirality : 0.041 0.164 4717 Planarity : 0.004 0.107 5203 Dihedral : 13.235 148.971 4669 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.69 % Allowed : 13.14 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3587 helix: 1.61 (0.14), residues: 1447 sheet: -1.47 (0.20), residues: 624 loop : -0.81 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 6 614 HIS 0.004 0.001 HIS 5 540 PHE 0.024 0.001 PHE 5 393 TYR 0.017 0.001 TYR 2 535 ARG 0.016 0.000 ARG 3 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7174 Ramachandran restraints generated. 3587 Oldfield, 0 Emsley, 3587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 530 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 285 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 222 MET cc_start: 0.8458 (mmp) cc_final: 0.8203 (mmp) REVERT: 2 284 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.6989 (mmt180) REVERT: 2 572 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7334 (mm-30) REVERT: 2 621 GLN cc_start: 0.7786 (pt0) cc_final: 0.7502 (pt0) REVERT: 3 38 GLU cc_start: 0.9427 (tp30) cc_final: 0.9166 (tp30) REVERT: 3 633 MET cc_start: 0.8913 (mmt) cc_final: 0.8611 (mmt) REVERT: 4 162 CYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7942 (m) REVERT: 4 294 GLN cc_start: 0.8669 (pt0) cc_final: 0.8308 (pm20) REVERT: 4 543 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8823 (tp) REVERT: 5 129 LYS cc_start: 0.9460 (ptpt) cc_final: 0.9147 (ptpp) REVERT: 5 320 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: 7 102 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8143 (t80) REVERT: 7 269 ASP cc_start: 0.7994 (m-30) cc_final: 0.7655 (m-30) outliers start: 54 outliers final: 44 residues processed: 325 average time/residue: 0.8159 time to fit residues: 425.8564 Evaluate side-chains 327 residues out of total 3188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLU Chi-restraints excluded: chain 2 residue 284 ARG Chi-restraints excluded: chain 2 residue 309 SER Chi-restraints excluded: chain 2 residue 315 CYS Chi-restraints excluded: chain 2 residue 345 GLN Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 379 GLN Chi-restraints excluded: chain 2 residue 463 MET Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 539 VAL Chi-restraints excluded: chain 2 residue 593 ASN Chi-restraints excluded: chain 2 residue 605 GLU Chi-restraints excluded: chain 2 residue 625 THR Chi-restraints excluded: chain 2 residue 735 LEU Chi-restraints excluded: chain 2 residue 762 ILE Chi-restraints excluded: chain 2 residue 780 ILE Chi-restraints excluded: chain 2 residue 822 LEU Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 122 SER Chi-restraints excluded: chain 3 residue 130 ILE Chi-restraints excluded: chain 3 residue 290 THR Chi-restraints excluded: chain 3 residue 373 SER Chi-restraints excluded: chain 3 residue 610 THR Chi-restraints excluded: chain 3 residue 646 VAL Chi-restraints excluded: chain 4 residue 115 ARG Chi-restraints excluded: chain 4 residue 162 CYS Chi-restraints excluded: chain 4 residue 247 ASP Chi-restraints excluded: chain 4 residue 256 HIS Chi-restraints excluded: chain 4 residue 266 LEU Chi-restraints excluded: chain 4 residue 505 ASN Chi-restraints excluded: chain 4 residue 543 LEU Chi-restraints excluded: chain 4 residue 586 VAL Chi-restraints excluded: chain 4 residue 669 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 209 LEU Chi-restraints excluded: chain 5 residue 258 VAL Chi-restraints excluded: chain 5 residue 272 LYS Chi-restraints excluded: chain 5 residue 276 LEU Chi-restraints excluded: chain 5 residue 291 SER Chi-restraints excluded: chain 5 residue 320 GLU Chi-restraints excluded: chain 5 residue 404 THR Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 520 VAL Chi-restraints excluded: chain 6 residue 75 LEU Chi-restraints excluded: chain 6 residue 553 VAL Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 7 residue 102 TYR Chi-restraints excluded: chain 7 residue 234 GLU Chi-restraints excluded: chain 7 residue 404 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3248 > 50: distance: 69 - 349: 34.504 distance: 72 - 346: 31.775 distance: 95 - 319: 32.337 distance: 98 - 316: 34.450 distance: 217 - 226: 30.927 distance: 226 - 227: 11.626 distance: 226 - 233: 40.066 distance: 227 - 228: 33.908 distance: 227 - 230: 13.656 distance: 227 - 234: 33.140 distance: 228 - 242: 38.610 distance: 230 - 231: 42.416 distance: 230 - 232: 37.498 distance: 230 - 235: 33.380 distance: 231 - 236: 7.753 distance: 231 - 237: 8.878 distance: 231 - 238: 7.649 distance: 232 - 239: 18.769 distance: 232 - 240: 19.676 distance: 232 - 241: 19.785 distance: 242 - 243: 58.323 distance: 242 - 251: 40.058 distance: 243 - 244: 41.838 distance: 243 - 246: 20.557 distance: 243 - 252: 13.603 distance: 244 - 245: 7.252 distance: 244 - 259: 46.648 distance: 246 - 247: 21.511 distance: 246 - 253: 25.839 distance: 246 - 254: 23.776 distance: 247 - 248: 53.445 distance: 247 - 255: 29.769 distance: 247 - 256: 14.621 distance: 248 - 249: 12.686 distance: 248 - 250: 38.839 distance: 250 - 257: 41.996 distance: 250 - 258: 5.017 distance: 259 - 260: 39.804 distance: 259 - 265: 48.733 distance: 260 - 261: 52.475 distance: 260 - 263: 65.960 distance: 260 - 266: 53.219 distance: 261 - 262: 6.813 distance: 261 - 273: 43.495 distance: 263 - 264: 67.739 distance: 263 - 267: 37.841 distance: 263 - 268: 49.080 distance: 264 - 265: 67.309 distance: 264 - 269: 36.325 distance: 264 - 270: 46.525 distance: 265 - 271: 20.988 distance: 265 - 272: 36.432 distance: 273 - 274: 12.439 distance: 273 - 277: 25.558 distance: 274 - 275: 15.624 distance: 274 - 278: 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