Starting phenix.real_space_refine on Sat Oct 11 02:15:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd2_36173/10_2025/8jd2_36173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd2_36173/10_2025/8jd2_36173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd2_36173/10_2025/8jd2_36173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd2_36173/10_2025/8jd2_36173.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd2_36173/10_2025/8jd2_36173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd2_36173/10_2025/8jd2_36173.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6749 2.51 5 N 1885 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10730 Number of models: 1 Model: "" Number of chains: 6 Chain: "2" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5258 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 34, 'TRANS': 715} Chain breaks: 3 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 795 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 14, 'GLN:plan1': 5, 'ASP:plan': 4, 'HIS:plan': 4, 'ASN:plan1': 7, 'TYR:plan': 11, 'PHE:plan': 12, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 362 Chain: "3" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5424 Classifications: {'peptide': 749} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 29, 'TRANS': 719} Chain breaks: 3 Unresolved non-hydrogen bonds: 547 Unresolved non-hydrogen angles: 695 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ARG:plan': 6, 'HIS:plan': 3, 'ASP:plan': 5, 'TYR:plan': 8, 'TRP:plan': 3, 'PHE:plan': 13} Unresolved non-hydrogen planarities: 294 Chain: "2" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "2" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "3" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 10730 At special positions: 0 Unit cell: (106.029, 93.177, 177.786, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2026 8.00 N 1885 7.00 C 6749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 21102 " - " ASN 2 203 " " NAG 31002 " - " ASN 3 209 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 536.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 46.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain '2' and resid 58 through 74 Processing helix chain '2' and resid 94 through 108 removed outlier: 4.348A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 2 108 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 156 Processing helix chain '2' and resid 169 through 174 removed outlier: 3.512A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 202 removed outlier: 3.880A pdb=" N GLN 2 191 " --> pdb=" O PRO 2 187 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE 2 202 " --> pdb=" O ILE 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 231 removed outlier: 4.037A pdb=" N THR 2 219 " --> pdb=" O ASP 2 215 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 324 through 333 Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 375 through 377 No H-bonds generated for 'chain '2' and resid 375 through 377' Processing helix chain '2' and resid 378 through 400 Processing helix chain '2' and resid 414 through 422 removed outlier: 3.654A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 482 through 485 Processing helix chain '2' and resid 489 through 493 Processing helix chain '2' and resid 568 through 593 Processing helix chain '2' and resid 604 through 624 removed outlier: 3.745A pdb=" N GLY 2 611 " --> pdb=" O TYR 2 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS 2 618 " --> pdb=" O PHE 2 614 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR 2 620 " --> pdb=" O CYS 2 616 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) Processing helix chain '2' and resid 631 through 657 removed outlier: 3.953A pdb=" N ARG 2 635 " --> pdb=" O VAL 2 631 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG 2 636 " --> pdb=" O CYS 2 632 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU 2 637 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR 2 641 " --> pdb=" O LEU 2 637 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS 2 646 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 2 650 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) Processing helix chain '2' and resid 678 through 702 removed outlier: 3.753A pdb=" N GLN 2 690 " --> pdb=" O LEU 2 686 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE 2 693 " --> pdb=" O GLY 2 689 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 2 694 " --> pdb=" O GLN 2 690 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL 2 700 " --> pdb=" O ALA 2 696 " (cutoff:3.500A) Processing helix chain '2' and resid 721 through 750 removed outlier: 3.591A pdb=" N ASP 2 725 " --> pdb=" O CYS 2 721 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET 2 728 " --> pdb=" O ARG 2 724 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU 2 729 " --> pdb=" O ASP 2 725 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU 2 737 " --> pdb=" O ALA 2 733 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 2 738 " --> pdb=" O TYR 2 734 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR 2 745 " --> pdb=" O LEU 2 741 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA 2 746 " --> pdb=" O CYS 2 742 " (cutoff:3.500A) Processing helix chain '2' and resid 755 through 775 Processing helix chain '2' and resid 775 through 784 removed outlier: 3.855A pdb=" N ILE 2 779 " --> pdb=" O ALA 2 775 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR 2 781 " --> pdb=" O LEU 2 777 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL 2 782 " --> pdb=" O PRO 2 778 " (cutoff:3.500A) Processing helix chain '2' and resid 790 through 810 removed outlier: 3.968A pdb=" N MET 2 794 " --> pdb=" O GLN 2 790 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE 2 810 " --> pdb=" O LEU 2 806 " (cutoff:3.500A) Processing helix chain '3' and resid 61 through 66 removed outlier: 3.602A pdb=" N ILE 3 66 " --> pdb=" O GLU 3 62 " (cutoff:3.500A) Processing helix chain '3' and resid 66 through 81 Processing helix chain '3' and resid 101 through 115 removed outlier: 3.712A pdb=" N GLU 3 107 " --> pdb=" O THR 3 103 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 162 removed outlier: 3.559A pdb=" N LEU 3 160 " --> pdb=" O GLN 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 175 through 180 Processing helix chain '3' and resid 193 through 208 removed outlier: 4.012A pdb=" N GLN 3 197 " --> pdb=" O PRO 3 193 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 237 removed outlier: 3.685A pdb=" N LEU 3 236 " --> pdb=" O GLN 3 232 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG 3 237 " --> pdb=" O GLU 3 233 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 264 Processing helix chain '3' and resid 277 through 290 Processing helix chain '3' and resid 313 through 318 removed outlier: 3.735A pdb=" N ALA 3 317 " --> pdb=" O SER 3 313 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 338 removed outlier: 3.598A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 387 through 389 No H-bonds generated for 'chain '3' and resid 387 through 389' Processing helix chain '3' and resid 390 through 412 removed outlier: 3.521A pdb=" N THR 3 410 " --> pdb=" O LYS 3 406 " (cutoff:3.500A) Processing helix chain '3' and resid 419 through 423 Processing helix chain '3' and resid 426 through 434 Processing helix chain '3' and resid 449 through 451 No H-bonds generated for 'chain '3' and resid 449 through 451' Processing helix chain '3' and resid 494 through 497 Processing helix chain '3' and resid 574 through 597 removed outlier: 4.297A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix removed outlier: 3.525A pdb=" N LEU 3 586 " --> pdb=" O THR 3 582 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS 3 592 " --> pdb=" O PHE 3 588 " (cutoff:3.500A) Processing helix chain '3' and resid 614 through 622 Processing helix chain '3' and resid 622 through 633 removed outlier: 3.582A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 664 removed outlier: 3.833A pdb=" N LEU 3 643 " --> pdb=" O VAL 3 639 " (cutoff:3.500A) Processing helix chain '3' and resid 690 through 702 removed outlier: 3.547A pdb=" N VAL 3 701 " --> pdb=" O LEU 3 697 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET 3 702 " --> pdb=" O VAL 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 734 through 757 removed outlier: 3.887A pdb=" N LEU 3 738 " --> pdb=" O ASP 3 734 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 3 750 " --> pdb=" O ILE 3 746 " (cutoff:3.500A) Processing helix chain '3' and resid 766 through 783 removed outlier: 3.712A pdb=" N PHE 3 770 " --> pdb=" O ASN 3 766 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY 3 772 " --> pdb=" O ALA 3 768 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE 3 780 " --> pdb=" O TYR 3 776 " (cutoff:3.500A) Processing helix chain '3' and resid 795 through 827 removed outlier: 3.535A pdb=" N CYS 3 817 " --> pdb=" O VAL 3 813 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 26 through 28 removed outlier: 3.712A pdb=" N ALA 2 86 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN 2 162 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 41 through 43 removed outlier: 4.705A pdb=" N GLN 2 42 " --> pdb=" O GLY 2 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 241 removed outlier: 6.255A pdb=" N VAL 2 207 " --> pdb=" O VAL 2 235 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR 2 237 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N PHE 2 269 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL 2 210 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR 2 473 " --> pdb=" O THR 2 479 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR 2 479 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 427 through 429 removed outlier: 3.680A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 33 through 35 removed outlier: 6.292A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain '3' and resid 240 through 247 removed outlier: 7.872A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE 3 275 " --> pdb=" O SER 3 214 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL 3 216 " --> pdb=" O PHE 3 275 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL 3 474 " --> pdb=" O TYR 3 478 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 440 through 441 removed outlier: 3.503A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 518 through 521 removed outlier: 3.798A pdb=" N LYS 3 519 " --> pdb=" O ILE 3 532 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 539 through 540 removed outlier: 3.600A pdb=" N TYR 3 539 " --> pdb=" O MET 3 547 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 553 through 555 492 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3626 1.34 - 1.46: 2514 1.46 - 1.58: 4713 1.58 - 1.70: 1 1.70 - 1.82: 88 Bond restraints: 10942 Sorted by residual: bond pdb=" CG PRO 3 512 " pdb=" CD PRO 3 512 " ideal model delta sigma weight residual 1.503 1.589 -0.086 3.40e-02 8.65e+02 6.46e+00 bond pdb=" CB PRO 3 512 " pdb=" CG PRO 3 512 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.53e+00 bond pdb=" C GLU 31001 " pdb=" O GLU 31001 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.93e+00 bond pdb=" C GLU 21101 " pdb=" O GLU 21101 " ideal model delta sigma weight residual 1.231 1.259 -0.028 2.00e-02 2.50e+03 1.92e+00 bond pdb=" C GLU 31001 " pdb=" OXT GLU 31001 " ideal model delta sigma weight residual 1.231 1.258 -0.027 2.00e-02 2.50e+03 1.86e+00 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 14702 1.41 - 2.82: 179 2.82 - 4.23: 44 4.23 - 5.64: 11 5.64 - 7.05: 1 Bond angle restraints: 14937 Sorted by residual: angle pdb=" CA PRO 3 512 " pdb=" N PRO 3 512 " pdb=" CD PRO 3 512 " ideal model delta sigma weight residual 112.00 104.95 7.05 1.40e+00 5.10e-01 2.53e+01 angle pdb=" N VAL 2 597 " pdb=" CA VAL 2 597 " pdb=" C VAL 2 597 " ideal model delta sigma weight residual 113.53 110.56 2.97 9.80e-01 1.04e+00 9.19e+00 angle pdb=" C PRO 2 546 " pdb=" N ASN 2 547 " pdb=" CA ASN 2 547 " ideal model delta sigma weight residual 121.54 126.10 -4.56 1.91e+00 2.74e-01 5.70e+00 angle pdb=" CA VAL 3 639 " pdb=" C VAL 3 639 " pdb=" N ILE 3 640 " ideal model delta sigma weight residual 116.60 119.81 -3.21 1.45e+00 4.76e-01 4.89e+00 angle pdb=" CA VAL 2 597 " pdb=" C VAL 2 597 " pdb=" N VAL 2 598 " ideal model delta sigma weight residual 119.31 116.80 2.51 1.15e+00 7.56e-01 4.78e+00 ... (remaining 14932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.55: 6084 20.55 - 41.10: 384 41.10 - 61.66: 59 61.66 - 82.21: 33 82.21 - 102.76: 11 Dihedral angle restraints: 6571 sinusoidal: 2223 harmonic: 4348 Sorted by residual: dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual 93.00 10.10 82.90 1 1.00e+01 1.00e-02 8.41e+01 dihedral pdb=" CB CYS 3 240 " pdb=" SG CYS 3 240 " pdb=" SG CYS 3 527 " pdb=" CB CYS 3 527 " ideal model delta sinusoidal sigma weight residual 93.00 14.08 78.92 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS 3 534 " pdb=" SG CYS 3 534 " pdb=" SG CYS 3 546 " pdb=" CB CYS 3 546 " ideal model delta sinusoidal sigma weight residual -86.00 -164.34 78.34 1 1.00e+01 1.00e-02 7.66e+01 ... (remaining 6568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1559 0.062 - 0.124: 178 0.124 - 0.186: 3 0.186 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 1742 Sorted by residual: chirality pdb=" C1 NAG 31002 " pdb=" ND2 ASN 3 209 " pdb=" C2 NAG 31002 " pdb=" O5 NAG 31002 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" C1 NAG 21102 " pdb=" ND2 ASN 2 203 " pdb=" C2 NAG 21102 " pdb=" O5 NAG 21102 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" C4 NAG 21102 " pdb=" C3 NAG 21102 " pdb=" C5 NAG 21102 " pdb=" O4 NAG 21102 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1739 not shown) Planarity restraints: 1960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 3 511 " 0.071 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO 3 512 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO 3 512 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 3 512 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 2 411 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO 2 412 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 2 570 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO 2 571 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO 2 571 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO 2 571 " 0.023 5.00e-02 4.00e+02 ... (remaining 1957 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1224 2.75 - 3.29: 10401 3.29 - 3.83: 17679 3.83 - 4.36: 20514 4.36 - 4.90: 35220 Nonbonded interactions: 85038 Sorted by model distance: nonbonded pdb=" O4 NAG 21102 " pdb=" O7 NAG 21102 " model vdw 2.213 3.040 nonbonded pdb=" O4 NAG 31002 " pdb=" O7 NAG 31002 " model vdw 2.225 3.040 nonbonded pdb=" O TYR 3 212 " pdb=" OG SER 3 507 " model vdw 2.268 3.040 nonbonded pdb=" O ALA 2 170 " pdb=" OG SER 2 173 " model vdw 2.286 3.040 nonbonded pdb=" O MET 3 593 " pdb=" OG1 THR 3 596 " model vdw 2.286 3.040 ... (remaining 85033 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 0.086 10962 Z= 0.096 Angle : 0.450 8.411 14979 Z= 0.236 Chirality : 0.040 0.309 1742 Planarity : 0.004 0.104 1958 Dihedral : 14.981 102.759 3701 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.20 % Allowed : 10.10 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.22), residues: 1483 helix: 1.38 (0.21), residues: 624 sheet: -0.85 (0.40), residues: 172 loop : -1.69 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 368 TYR 0.011 0.001 TYR 3 186 PHE 0.005 0.001 PHE 2 67 TRP 0.011 0.001 TRP 2 487 HIS 0.004 0.000 HIS 2 365 Details of bonding type rmsd covalent geometry : bond 0.00220 (10942) covalent geometry : angle 0.43693 (14937) SS BOND : bond 0.00121 ( 18) SS BOND : angle 0.50887 ( 36) hydrogen bonds : bond 0.25258 ( 492) hydrogen bonds : angle 6.80127 ( 1431) link_NAG-ASN : bond 0.01377 ( 2) link_NAG-ASN : angle 5.36037 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.419 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.4977 time to fit residues: 60.5609 Evaluate side-chains 109 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.225587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.150715 restraints weight = 10997.565| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.35 r_work: 0.3358 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10962 Z= 0.136 Angle : 0.520 9.875 14979 Z= 0.269 Chirality : 0.042 0.253 1742 Planarity : 0.004 0.045 1958 Dihedral : 6.110 59.151 1646 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.31 % Allowed : 10.61 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.22), residues: 1483 helix: 1.63 (0.21), residues: 639 sheet: -1.10 (0.38), residues: 188 loop : -1.81 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 183 TYR 0.020 0.001 TYR 3 318 PHE 0.014 0.001 PHE 3 195 TRP 0.007 0.001 TRP 2 487 HIS 0.005 0.001 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00286 (10942) covalent geometry : angle 0.50377 (14937) SS BOND : bond 0.00157 ( 18) SS BOND : angle 0.58026 ( 36) hydrogen bonds : bond 0.05496 ( 492) hydrogen bonds : angle 4.62463 ( 1431) link_NAG-ASN : bond 0.01398 ( 2) link_NAG-ASN : angle 6.33994 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: 3 83 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7705 (p0) REVERT: 3 185 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: 3 465 ARG cc_start: 0.8301 (mtt-85) cc_final: 0.7842 (mtp-110) REVERT: 3 547 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5241 (pmm) REVERT: 3 590 CYS cc_start: 0.7649 (m) cc_final: 0.6788 (t) outliers start: 13 outliers final: 7 residues processed: 122 average time/residue: 0.5571 time to fit residues: 73.7887 Evaluate side-chains 115 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 199 LYS Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 547 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 140 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 56 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 338 ASN 3 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.222742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144763 restraints weight = 10982.336| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.24 r_work: 0.3297 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10962 Z= 0.136 Angle : 0.512 11.872 14979 Z= 0.264 Chirality : 0.042 0.258 1742 Planarity : 0.003 0.039 1958 Dihedral : 4.916 53.050 1646 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.22 % Allowed : 11.72 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.22), residues: 1483 helix: 1.67 (0.21), residues: 651 sheet: -1.18 (0.37), residues: 190 loop : -1.97 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 3 68 TYR 0.011 0.001 TYR 3 186 PHE 0.013 0.001 PHE 2 327 TRP 0.008 0.001 TRP 2 291 HIS 0.005 0.001 HIS 2 365 Details of bonding type rmsd covalent geometry : bond 0.00306 (10942) covalent geometry : angle 0.49097 (14937) SS BOND : bond 0.00136 ( 18) SS BOND : angle 0.62117 ( 36) hydrogen bonds : bond 0.04492 ( 492) hydrogen bonds : angle 4.16191 ( 1431) link_NAG-ASN : bond 0.01226 ( 2) link_NAG-ASN : angle 7.16253 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: 2 83 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7242 (ttm110) REVERT: 2 225 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: 3 83 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7894 (p0) REVERT: 3 101 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8294 (ptp-170) REVERT: 3 141 LEU cc_start: 0.7872 (tp) cc_final: 0.7647 (tp) REVERT: 3 185 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: 3 251 ASN cc_start: 0.6378 (m-40) cc_final: 0.5835 (OUTLIER) REVERT: 3 465 ARG cc_start: 0.8409 (mtt-85) cc_final: 0.7940 (mtp-110) REVERT: 3 590 CYS cc_start: 0.7782 (m) cc_final: 0.7016 (t) outliers start: 22 outliers final: 8 residues processed: 131 average time/residue: 0.5808 time to fit residues: 82.5505 Evaluate side-chains 121 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 101 ARG Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 139 optimal weight: 0.0020 chunk 121 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.214124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146515 restraints weight = 10916.865| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.77 r_work: 0.3254 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10962 Z= 0.138 Angle : 0.514 12.723 14979 Z= 0.264 Chirality : 0.042 0.233 1742 Planarity : 0.003 0.038 1958 Dihedral : 4.833 56.107 1646 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.63 % Allowed : 12.83 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.22), residues: 1483 helix: 1.75 (0.21), residues: 646 sheet: -1.21 (0.37), residues: 188 loop : -1.98 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 405 TYR 0.011 0.001 TYR 3 171 PHE 0.012 0.001 PHE 2 67 TRP 0.010 0.001 TRP 2 291 HIS 0.004 0.001 HIS 2 365 Details of bonding type rmsd covalent geometry : bond 0.00316 (10942) covalent geometry : angle 0.49334 (14937) SS BOND : bond 0.00145 ( 18) SS BOND : angle 0.59368 ( 36) hydrogen bonds : bond 0.04134 ( 492) hydrogen bonds : angle 4.01858 ( 1431) link_NAG-ASN : bond 0.01081 ( 2) link_NAG-ASN : angle 7.17236 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: 2 83 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: 2 183 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8219 (ttm170) REVERT: 2 225 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: 3 185 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: 3 377 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5980 (pp) REVERT: 3 494 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7879 (t) REVERT: 3 590 CYS cc_start: 0.7622 (m) cc_final: 0.6963 (t) outliers start: 26 outliers final: 10 residues processed: 132 average time/residue: 0.6314 time to fit residues: 89.9168 Evaluate side-chains 122 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 148 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.211747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.130743 restraints weight = 10816.353| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.65 r_work: 0.3139 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10962 Z= 0.199 Angle : 0.567 13.505 14979 Z= 0.293 Chirality : 0.043 0.249 1742 Planarity : 0.004 0.037 1958 Dihedral : 5.084 58.826 1646 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.23 % Allowed : 13.03 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.22), residues: 1483 helix: 1.66 (0.21), residues: 647 sheet: -1.21 (0.36), residues: 189 loop : -2.10 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 405 TYR 0.016 0.002 TYR 3 171 PHE 0.015 0.002 PHE 2 38 TRP 0.013 0.001 TRP 2 291 HIS 0.004 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00470 (10942) covalent geometry : angle 0.54487 (14937) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.74621 ( 36) hydrogen bonds : bond 0.04588 ( 492) hydrogen bonds : angle 4.07852 ( 1431) link_NAG-ASN : bond 0.00957 ( 2) link_NAG-ASN : angle 7.67639 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.424 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7088 (ttm110) REVERT: 2 183 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.8279 (ttm170) REVERT: 2 225 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: 3 219 GLU cc_start: 0.8521 (pt0) cc_final: 0.8303 (pt0) REVERT: 3 360 GLN cc_start: 0.7473 (mt0) cc_final: 0.6982 (mm110) REVERT: 3 465 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.8066 (mtm180) REVERT: 3 590 CYS cc_start: 0.7668 (m) cc_final: 0.7019 (t) outliers start: 32 outliers final: 13 residues processed: 138 average time/residue: 0.5973 time to fit residues: 89.2446 Evaluate side-chains 125 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 51 optimal weight: 0.0570 chunk 44 optimal weight: 0.0010 chunk 83 optimal weight: 0.9980 overall best weight: 0.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.213059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.136930 restraints weight = 10885.186| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.30 r_work: 0.3187 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10962 Z= 0.129 Angle : 0.509 12.668 14979 Z= 0.261 Chirality : 0.042 0.248 1742 Planarity : 0.003 0.038 1958 Dihedral : 4.875 57.499 1646 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.42 % Allowed : 14.04 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.22), residues: 1483 helix: 1.76 (0.21), residues: 648 sheet: -1.29 (0.36), residues: 188 loop : -2.08 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 405 TYR 0.013 0.001 TYR 3 186 PHE 0.011 0.001 PHE 2 67 TRP 0.010 0.001 TRP 2 291 HIS 0.004 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00295 (10942) covalent geometry : angle 0.48885 (14937) SS BOND : bond 0.00139 ( 18) SS BOND : angle 0.54387 ( 36) hydrogen bonds : bond 0.03888 ( 492) hydrogen bonds : angle 3.90593 ( 1431) link_NAG-ASN : bond 0.01189 ( 2) link_NAG-ASN : angle 6.98898 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: 2 83 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7054 (ttm110) REVERT: 2 183 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8224 (ttm170) REVERT: 2 225 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: 3 185 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: 3 219 GLU cc_start: 0.8513 (pt0) cc_final: 0.8269 (pt0) REVERT: 3 360 GLN cc_start: 0.7466 (mt0) cc_final: 0.6994 (mm110) REVERT: 3 465 ARG cc_start: 0.8419 (mtt-85) cc_final: 0.8004 (mtm180) REVERT: 3 488 GLU cc_start: 0.7172 (mp0) cc_final: 0.6701 (mt-10) REVERT: 3 494 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7590 (t) REVERT: 3 590 CYS cc_start: 0.7736 (m) cc_final: 0.7078 (t) outliers start: 24 outliers final: 11 residues processed: 135 average time/residue: 0.6246 time to fit residues: 90.8771 Evaluate side-chains 127 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 540 LEU Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 30.0000 chunk 41 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 292 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.211674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132449 restraints weight = 10958.011| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.14 r_work: 0.3147 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10962 Z= 0.172 Angle : 0.544 12.826 14979 Z= 0.281 Chirality : 0.043 0.250 1742 Planarity : 0.004 0.037 1958 Dihedral : 4.990 57.455 1646 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.63 % Allowed : 14.44 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1483 helix: 1.76 (0.21), residues: 648 sheet: -1.18 (0.36), residues: 187 loop : -2.14 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 405 TYR 0.014 0.002 TYR 3 171 PHE 0.013 0.002 PHE 2 38 TRP 0.013 0.001 TRP 2 291 HIS 0.006 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00404 (10942) covalent geometry : angle 0.52359 (14937) SS BOND : bond 0.00174 ( 18) SS BOND : angle 0.67139 ( 36) hydrogen bonds : bond 0.04262 ( 492) hydrogen bonds : angle 3.93802 ( 1431) link_NAG-ASN : bond 0.00992 ( 2) link_NAG-ASN : angle 7.23124 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.396 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7038 (ttm110) REVERT: 2 183 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.8291 (ttm170) REVERT: 2 225 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8010 (mt-10) REVERT: 3 219 GLU cc_start: 0.8547 (pt0) cc_final: 0.8321 (pt0) REVERT: 3 360 GLN cc_start: 0.7457 (mt0) cc_final: 0.6976 (mm110) REVERT: 3 465 ARG cc_start: 0.8422 (mtt-85) cc_final: 0.8037 (mtm180) REVERT: 3 494 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7583 (t) REVERT: 3 508 GLN cc_start: 0.6993 (mt0) cc_final: 0.6452 (pt0) REVERT: 3 590 CYS cc_start: 0.7718 (m) cc_final: 0.7096 (t) outliers start: 26 outliers final: 14 residues processed: 132 average time/residue: 0.6057 time to fit residues: 86.1886 Evaluate side-chains 125 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.0170 chunk 140 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 26 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 447 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.213395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.137366 restraints weight = 10867.318| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.49 r_work: 0.3191 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10962 Z= 0.118 Angle : 0.501 12.165 14979 Z= 0.258 Chirality : 0.041 0.255 1742 Planarity : 0.003 0.038 1958 Dihedral : 4.822 56.383 1646 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.22 % Allowed : 15.56 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.22), residues: 1483 helix: 1.86 (0.21), residues: 648 sheet: -1.25 (0.36), residues: 186 loop : -2.09 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 405 TYR 0.012 0.001 TYR 3 186 PHE 0.012 0.001 PHE 3 74 TRP 0.009 0.001 TRP 2 291 HIS 0.003 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00267 (10942) covalent geometry : angle 0.48247 (14937) SS BOND : bond 0.00134 ( 18) SS BOND : angle 0.53590 ( 36) hydrogen bonds : bond 0.03691 ( 492) hydrogen bonds : angle 3.80308 ( 1431) link_NAG-ASN : bond 0.01209 ( 2) link_NAG-ASN : angle 6.70413 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: 2 83 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7025 (ttm110) REVERT: 2 183 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8227 (ttm170) REVERT: 2 225 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7935 (mt-10) REVERT: 3 219 GLU cc_start: 0.8510 (pt0) cc_final: 0.8276 (pt0) REVERT: 3 360 GLN cc_start: 0.7391 (mt0) cc_final: 0.6936 (mm110) REVERT: 3 488 GLU cc_start: 0.7136 (mp0) cc_final: 0.6783 (mt-10) REVERT: 3 494 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7593 (t) REVERT: 3 590 CYS cc_start: 0.7759 (m) cc_final: 0.7148 (t) outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 0.5891 time to fit residues: 82.9047 Evaluate side-chains 127 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 67 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 315 HIS 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.211411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130414 restraints weight = 10914.554| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.38 r_work: 0.3128 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10962 Z= 0.183 Angle : 0.553 12.477 14979 Z= 0.286 Chirality : 0.043 0.247 1742 Planarity : 0.004 0.037 1958 Dihedral : 5.006 56.284 1646 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.22), residues: 1483 helix: 1.80 (0.21), residues: 648 sheet: -1.22 (0.36), residues: 187 loop : -2.15 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 405 TYR 0.013 0.002 TYR 3 171 PHE 0.013 0.002 PHE 2 67 TRP 0.013 0.001 TRP 2 291 HIS 0.005 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00432 (10942) covalent geometry : angle 0.53445 (14937) SS BOND : bond 0.00197 ( 18) SS BOND : angle 0.68997 ( 36) hydrogen bonds : bond 0.04289 ( 492) hydrogen bonds : angle 3.89246 ( 1431) link_NAG-ASN : bond 0.00910 ( 2) link_NAG-ASN : angle 7.09718 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.404 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7072 (ttm110) REVERT: 2 183 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8306 (ttm170) REVERT: 2 225 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8067 (mt-10) REVERT: 3 219 GLU cc_start: 0.8569 (pt0) cc_final: 0.8349 (pt0) REVERT: 3 360 GLN cc_start: 0.7371 (mt0) cc_final: 0.6883 (mm110) REVERT: 3 465 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8136 (mtm180) REVERT: 3 494 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7597 (t) REVERT: 3 590 CYS cc_start: 0.7692 (m) cc_final: 0.7070 (t) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.6144 time to fit residues: 85.7050 Evaluate side-chains 126 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 310 ILE Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 453 ILE Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 57 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 38 optimal weight: 0.0000 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.212776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135757 restraints weight = 10898.081| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.04 r_work: 0.3204 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10962 Z= 0.130 Angle : 0.516 12.024 14979 Z= 0.267 Chirality : 0.042 0.254 1742 Planarity : 0.004 0.038 1958 Dihedral : 4.868 55.946 1646 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.22 % Allowed : 16.26 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.22), residues: 1483 helix: 1.88 (0.21), residues: 648 sheet: -1.23 (0.36), residues: 187 loop : -2.11 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 405 TYR 0.013 0.001 TYR 3 186 PHE 0.012 0.001 PHE 3 74 TRP 0.010 0.001 TRP 2 291 HIS 0.003 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00298 (10942) covalent geometry : angle 0.49834 (14937) SS BOND : bond 0.00148 ( 18) SS BOND : angle 0.57193 ( 36) hydrogen bonds : bond 0.03767 ( 492) hydrogen bonds : angle 3.78296 ( 1431) link_NAG-ASN : bond 0.01117 ( 2) link_NAG-ASN : angle 6.64843 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2966 Ramachandran restraints generated. 1483 Oldfield, 0 Emsley, 1483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.421 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6895 (ttm110) REVERT: 2 183 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8199 (ttm170) REVERT: 2 225 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: 3 219 GLU cc_start: 0.8480 (pt0) cc_final: 0.8248 (pt0) REVERT: 3 360 GLN cc_start: 0.7265 (mt0) cc_final: 0.6773 (mm110) REVERT: 3 407 MET cc_start: 0.8447 (ttt) cc_final: 0.8193 (ttt) REVERT: 3 488 GLU cc_start: 0.7059 (mp0) cc_final: 0.6694 (mt-10) REVERT: 3 494 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7502 (t) REVERT: 3 590 CYS cc_start: 0.7718 (m) cc_final: 0.7163 (t) outliers start: 22 outliers final: 16 residues processed: 126 average time/residue: 0.6067 time to fit residues: 82.7632 Evaluate side-chains 127 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 183 ARG Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 310 ILE Chi-restraints excluded: chain 3 residue 377 LEU Chi-restraints excluded: chain 3 residue 382 SER Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 441 THR Chi-restraints excluded: chain 3 residue 453 ILE Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 527 CYS Chi-restraints excluded: chain 3 residue 726 VAL Chi-restraints excluded: chain 3 residue 791 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 140 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.210075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130957 restraints weight = 10901.111| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.40 r_work: 0.3131 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 10962 Z= 0.236 Angle : 0.599 12.639 14979 Z= 0.311 Chirality : 0.045 0.252 1742 Planarity : 0.004 0.037 1958 Dihedral : 5.180 56.287 1646 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.32 % Allowed : 15.86 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.22), residues: 1483 helix: 1.73 (0.21), residues: 647 sheet: -1.34 (0.35), residues: 187 loop : -2.19 (0.22), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 2 405 TYR 0.017 0.002 TYR 3 171 PHE 0.016 0.002 PHE 2 38 TRP 0.017 0.002 TRP 2 291 HIS 0.006 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00563 (10942) covalent geometry : angle 0.58023 (14937) SS BOND : bond 0.00253 ( 18) SS BOND : angle 0.81370 ( 36) hydrogen bonds : bond 0.04684 ( 492) hydrogen bonds : angle 3.97440 ( 1431) link_NAG-ASN : bond 0.00752 ( 2) link_NAG-ASN : angle 7.26234 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5322.13 seconds wall clock time: 91 minutes 3.05 seconds (5463.05 seconds total)