Starting phenix.real_space_refine on Tue Jul 29 00:19:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd2_36173/07_2025/8jd2_36173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd2_36173/07_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_36173/07_2025/8jd2_36173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd2_36173/07_2025/8jd2_36173.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd2_36173/07_2025/8jd2_36173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd2_36173/07_2025/8jd2_36173.cif" } resolution = 2.8 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= 0.048 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 12, 'GLU:plan': 13, 'ARG:plan': 14} 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: {'GLN:plan1': 3, 'ARG:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 13, 'GLU:plan': 10, 'ASP:plan': 5} 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: 7.20, per 1000 atoms: 0.67 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.48 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: 3.32 Time building geometry restraints manager: 3.87 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: 2.430 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- 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 : 4.22 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 (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: -0.38 (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 TRP 0.011 0.001 TRP 2 487 HIS 0.004 0.000 HIS 2 365 PHE 0.005 0.001 PHE 2 67 TYR 0.011 0.001 TYR 3 186 ARG 0.003 0.000 ARG 2 368 Details of bonding type rmsd link_NAG-ASN : bond 0.01377 ( 2) link_NAG-ASN : angle 5.36037 ( 6) hydrogen bonds : bond 0.25258 ( 492) hydrogen bonds : angle 6.80127 ( 1431) SS BOND : bond 0.00121 ( 18) SS BOND : angle 0.50887 ( 36) covalent geometry : bond 0.00220 (10942) covalent geometry : angle 0.43693 (14937) *********************** 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 : 1.146 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 1.1341 time to fit residues: 138.7999 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 : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 56 HIS 2 283 GLN 3 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.211963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129329 restraints weight = 10788.346| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.43 r_work: 0.3135 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10962 Z= 0.256 Angle : 0.648 11.669 14979 Z= 0.338 Chirality : 0.046 0.264 1742 Planarity : 0.005 0.053 1958 Dihedral : 6.260 59.609 1646 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.22 % Allowed : 10.91 % Favored : 86.87 % 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: -0.69 (0.22), residues: 1483 helix: 1.26 (0.20), residues: 635 sheet: -1.36 (0.36), residues: 188 loop : -1.96 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 291 HIS 0.007 0.002 HIS 2 365 PHE 0.019 0.003 PHE 2 38 TYR 0.019 0.002 TYR 3 318 ARG 0.006 0.001 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.01038 ( 2) link_NAG-ASN : angle 7.69039 ( 6) hydrogen bonds : bond 0.06058 ( 492) hydrogen bonds : angle 4.72460 ( 1431) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.93236 ( 36) covalent geometry : bond 0.00599 (10942) covalent geometry : angle 0.62836 (14937) *********************** 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 138 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 1.136 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7159 (ttm110) REVERT: 2 225 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: 3 83 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7707 (p0) REVERT: 3 228 GLU cc_start: 0.8592 (tt0) cc_final: 0.8147 (tt0) REVERT: 3 465 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.7994 (mtm180) REVERT: 3 547 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5324 (pmm) REVERT: 3 590 CYS cc_start: 0.7714 (m) cc_final: 0.6891 (t) outliers start: 22 outliers final: 8 residues processed: 132 average time/residue: 1.3814 time to fit residues: 197.9514 Evaluate side-chains 117 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 59 ARG Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 199 LYS 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 547 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 338 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 = 0.4303 r_free = 0.4303 target = 0.214315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3480 r_free = 0.3480 target = 0.136098 restraints weight = 10821.129| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.16 r_work: 0.3175 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10962 Z= 0.125 Angle : 0.509 12.072 14979 Z= 0.263 Chirality : 0.042 0.259 1742 Planarity : 0.003 0.039 1958 Dihedral : 5.020 55.731 1646 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.02 % Allowed : 12.93 % Favored : 85.05 % 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: -0.52 (0.22), residues: 1483 helix: 1.53 (0.21), residues: 640 sheet: -1.28 (0.36), residues: 189 loop : -2.05 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 291 HIS 0.004 0.001 HIS 3 485 PHE 0.011 0.001 PHE 2 67 TYR 0.010 0.001 TYR 3 171 ARG 0.005 0.000 ARG 2 405 Details of bonding type rmsd link_NAG-ASN : bond 0.01326 ( 2) link_NAG-ASN : angle 7.09602 ( 6) hydrogen bonds : bond 0.04500 ( 492) hydrogen bonds : angle 4.21954 ( 1431) SS BOND : bond 0.00129 ( 18) SS BOND : angle 0.54881 ( 36) covalent geometry : bond 0.00275 (10942) covalent geometry : angle 0.48841 (14937) *********************** 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 131 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.775 Fit side-chains revert: symmetry clash REVERT: 2 83 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7105 (ttm110) REVERT: 2 218 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: 2 225 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: 3 83 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7792 (p0) REVERT: 3 141 LEU cc_start: 0.7834 (tp) cc_final: 0.7609 (tp) REVERT: 3 228 GLU cc_start: 0.8484 (tt0) cc_final: 0.8043 (tt0) REVERT: 3 377 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5769 (pp) REVERT: 3 494 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7821 (t) REVERT: 3 590 CYS cc_start: 0.7722 (m) cc_final: 0.7040 (t) outliers start: 20 outliers final: 8 residues processed: 125 average time/residue: 1.5416 time to fit residues: 210.6475 Evaluate side-chains 118 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 218 GLU Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 63 ASP Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 251 ASN Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 377 LEU 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 791 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 74 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 118 optimal weight: 0.2980 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.213579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134739 restraints weight = 10789.578| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.34 r_work: 0.3168 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10962 Z= 0.136 Angle : 0.512 12.972 14979 Z= 0.263 Chirality : 0.042 0.242 1742 Planarity : 0.003 0.038 1958 Dihedral : 4.864 56.737 1646 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.13 % Allowed : 12.53 % Favored : 84.34 % 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: -0.41 (0.22), residues: 1483 helix: 1.68 (0.21), residues: 645 sheet: -1.27 (0.36), residues: 188 loop : -2.07 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 291 HIS 0.004 0.001 HIS 3 485 PHE 0.012 0.001 PHE 2 67 TYR 0.012 0.001 TYR 3 186 ARG 0.002 0.000 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.01111 ( 2) link_NAG-ASN : angle 7.33696 ( 6) hydrogen bonds : bond 0.04160 ( 492) hydrogen bonds : angle 4.02121 ( 1431) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.54251 ( 36) covalent geometry : bond 0.00310 (10942) covalent geometry : angle 0.49043 (14937) *********************** 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 138 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.227 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7118 (ttm110) REVERT: 2 183 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.7961 (ttm110) REVERT: 2 218 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7836 (mm-30) REVERT: 2 225 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: 3 83 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7864 (p0) REVERT: 3 219 GLU cc_start: 0.8514 (pt0) cc_final: 0.8269 (pt0) REVERT: 3 377 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5873 (pp) REVERT: 3 465 ARG cc_start: 0.8438 (mtt-85) cc_final: 0.8146 (mtm180) REVERT: 3 494 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7789 (t) REVERT: 3 590 CYS cc_start: 0.7681 (m) cc_final: 0.7019 (t) outliers start: 31 outliers final: 10 residues processed: 133 average time/residue: 1.5960 time to fit residues: 230.1280 Evaluate side-chains 121 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 218 GLU 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 251 ASN 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 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 57 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 69 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 148 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.212238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132847 restraints weight = 10820.867| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.38 r_work: 0.3167 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10962 Z= 0.150 Angle : 0.524 12.768 14979 Z= 0.270 Chirality : 0.042 0.252 1742 Planarity : 0.004 0.038 1958 Dihedral : 4.923 58.074 1646 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.03 % Allowed : 13.84 % Favored : 83.13 % 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: -0.40 (0.22), residues: 1483 helix: 1.68 (0.21), residues: 647 sheet: -1.11 (0.37), residues: 180 loop : -2.10 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 291 HIS 0.005 0.001 HIS 3 485 PHE 0.012 0.002 PHE 2 67 TYR 0.013 0.001 TYR 3 186 ARG 0.003 0.000 ARG 2 405 Details of bonding type rmsd link_NAG-ASN : bond 0.01147 ( 2) link_NAG-ASN : angle 7.19720 ( 6) hydrogen bonds : bond 0.04154 ( 492) hydrogen bonds : angle 3.99060 ( 1431) SS BOND : bond 0.00168 ( 18) SS BOND : angle 0.60124 ( 36) covalent geometry : bond 0.00346 (10942) covalent geometry : angle 0.50340 (14937) *********************** 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 139 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.516 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7003 (ttm110) REVERT: 2 183 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.7967 (ttm110) REVERT: 2 218 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: 2 225 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: 2 410 MET cc_start: 0.7229 (ttt) cc_final: 0.6969 (ttt) REVERT: 3 83 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7799 (p0) REVERT: 3 219 GLU cc_start: 0.8501 (pt0) cc_final: 0.8261 (pt0) REVERT: 3 360 GLN cc_start: 0.7435 (mt0) cc_final: 0.6935 (mm110) REVERT: 3 377 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5779 (pp) REVERT: 3 407 MET cc_start: 0.8504 (ttt) cc_final: 0.8286 (ttt) REVERT: 3 465 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.7993 (mtm180) REVERT: 3 494 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7582 (t) REVERT: 3 590 CYS cc_start: 0.7746 (m) cc_final: 0.7095 (t) outliers start: 30 outliers final: 13 residues processed: 132 average time/residue: 1.7501 time to fit residues: 255.1181 Evaluate side-chains 130 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 3.950 ------------------------------------------------------------------------------- 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 218 GLU 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 83 ASP Chi-restraints excluded: chain 3 residue 251 ASN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 103 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 62 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 390 HIS 3 292 ASN 3 315 HIS 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.210146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.138937 restraints weight = 10876.760| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.22 r_work: 0.3183 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10962 Z= 0.218 Angle : 0.583 13.013 14979 Z= 0.302 Chirality : 0.044 0.253 1742 Planarity : 0.004 0.037 1958 Dihedral : 5.211 59.494 1646 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.74 % Allowed : 13.94 % Favored : 82.32 % 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: -0.48 (0.22), residues: 1483 helix: 1.67 (0.21), residues: 639 sheet: -1.29 (0.35), residues: 189 loop : -2.13 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 2 291 HIS 0.006 0.001 HIS 3 485 PHE 0.016 0.002 PHE 2 38 TYR 0.015 0.002 TYR 3 171 ARG 0.003 0.000 ARG 2 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00856 ( 2) link_NAG-ASN : angle 7.61527 ( 6) hydrogen bonds : bond 0.04715 ( 492) hydrogen bonds : angle 4.09747 ( 1431) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.75284 ( 36) covalent geometry : bond 0.00519 (10942) covalent geometry : angle 0.56272 (14937) *********************** 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 144 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 1.873 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6896 (ttm110) REVERT: 2 183 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8221 (ttm110) REVERT: 2 218 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: 2 225 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7939 (mt-10) REVERT: 2 226 LEU cc_start: 0.8367 (tt) cc_final: 0.7673 (mp) REVERT: 3 83 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7743 (p0) REVERT: 3 101 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8230 (ptp-170) REVERT: 3 219 GLU cc_start: 0.8479 (pt0) cc_final: 0.8266 (pt0) REVERT: 3 360 GLN cc_start: 0.7441 (mt0) cc_final: 0.6938 (mm110) REVERT: 3 465 ARG cc_start: 0.8315 (mtt-85) cc_final: 0.7929 (mtm180) REVERT: 3 493 ASP cc_start: 0.7952 (t0) cc_final: 0.7726 (t0) REVERT: 3 508 GLN cc_start: 0.6985 (mt0) cc_final: 0.6434 (pt0) REVERT: 3 590 CYS cc_start: 0.7674 (m) cc_final: 0.7059 (t) outliers start: 37 outliers final: 18 residues processed: 138 average time/residue: 1.4370 time to fit residues: 217.1782 Evaluate side-chains 129 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 218 GLU Chi-restraints excluded: chain 2 residue 225 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 2 residue 597 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 101 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 36 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 341 ASN 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.212736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.136352 restraints weight = 11085.197| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.17 r_work: 0.3187 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10962 Z= 0.119 Angle : 0.500 11.844 14979 Z= 0.258 Chirality : 0.041 0.264 1742 Planarity : 0.003 0.038 1958 Dihedral : 4.893 57.701 1646 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.63 % Allowed : 15.05 % Favored : 82.32 % 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: -0.35 (0.22), residues: 1483 helix: 1.75 (0.21), residues: 648 sheet: -1.07 (0.37), residues: 178 loop : -2.14 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 291 HIS 0.003 0.001 HIS 3 485 PHE 0.013 0.001 PHE 3 74 TYR 0.013 0.001 TYR 3 186 ARG 0.003 0.000 ARG 2 405 Details of bonding type rmsd link_NAG-ASN : bond 0.01209 ( 2) link_NAG-ASN : angle 6.68741 ( 6) hydrogen bonds : bond 0.03756 ( 492) hydrogen bonds : angle 3.87883 ( 1431) SS BOND : bond 0.00142 ( 18) SS BOND : angle 0.52324 ( 36) covalent geometry : bond 0.00269 (10942) covalent geometry : angle 0.48177 (14937) *********************** 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 139 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.073 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7007 (ttm110) REVERT: 2 183 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.7881 (ttm110) REVERT: 2 225 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: 3 83 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7824 (p0) REVERT: 3 219 GLU cc_start: 0.8513 (pt0) cc_final: 0.8297 (pt0) REVERT: 3 360 GLN cc_start: 0.7345 (mt0) cc_final: 0.6871 (mm110) REVERT: 3 407 MET cc_start: 0.8525 (ttt) cc_final: 0.8316 (ttt) REVERT: 3 465 ARG cc_start: 0.8451 (mtt-85) cc_final: 0.8014 (mtm180) REVERT: 3 488 GLU cc_start: 0.7163 (mp0) cc_final: 0.6677 (mt-10) REVERT: 3 493 ASP cc_start: 0.7977 (t0) cc_final: 0.7761 (t0) REVERT: 3 590 CYS cc_start: 0.7720 (m) cc_final: 0.7094 (t) outliers start: 26 outliers final: 17 residues processed: 134 average time/residue: 1.1481 time to fit residues: 167.0024 Evaluate side-chains 129 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 63 ASP Chi-restraints excluded: chain 3 residue 83 ASP Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 251 ASN 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 453 ILE 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 136 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 414 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 = 0.4251 r_free = 0.4251 target = 0.207419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123099 restraints weight = 10856.251| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.38 r_work: 0.3060 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 10962 Z= 0.395 Angle : 0.729 13.230 14979 Z= 0.379 Chirality : 0.051 0.261 1742 Planarity : 0.005 0.040 1958 Dihedral : 5.580 58.050 1646 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.54 % Allowed : 14.85 % Favored : 81.62 % 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: -0.70 (0.22), residues: 1483 helix: 1.47 (0.21), residues: 637 sheet: -1.28 (0.35), residues: 189 loop : -2.26 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP 2 291 HIS 0.007 0.002 HIS 3 485 PHE 0.027 0.003 PHE 2 38 TYR 0.024 0.003 TYR 3 171 ARG 0.005 0.001 ARG 2 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 2) link_NAG-ASN : angle 8.11702 ( 6) hydrogen bonds : bond 0.05863 ( 492) hydrogen bonds : angle 4.31890 ( 1431) SS BOND : bond 0.00413 ( 18) SS BOND : angle 1.15911 ( 36) covalent geometry : bond 0.00946 (10942) covalent geometry : angle 0.70921 (14937) *********************** 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 144 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.236 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.6987 (ttm110) REVERT: 2 146 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7901 (p0) REVERT: 2 183 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.7979 (ttm110) REVERT: 2 225 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: 2 226 LEU cc_start: 0.8502 (tt) cc_final: 0.7834 (mp) REVERT: 2 243 ARG cc_start: 0.7500 (mpt-90) cc_final: 0.6433 (mmp-170) REVERT: 3 83 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (p0) REVERT: 3 228 GLU cc_start: 0.8425 (tt0) cc_final: 0.7979 (tt0) REVERT: 3 360 GLN cc_start: 0.7409 (mt0) cc_final: 0.6890 (mm110) REVERT: 3 465 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8055 (mtm180) REVERT: 3 493 ASP cc_start: 0.8149 (t0) cc_final: 0.7907 (t0) REVERT: 3 494 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7611 (t) REVERT: 3 508 GLN cc_start: 0.6944 (mt0) cc_final: 0.6400 (pt0) REVERT: 3 590 CYS cc_start: 0.7775 (m) cc_final: 0.7249 (t) outliers start: 35 outliers final: 18 residues processed: 135 average time/residue: 1.2549 time to fit residues: 183.3856 Evaluate side-chains 130 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 146 ASP 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 426 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 63 ASP Chi-restraints excluded: chain 3 residue 83 ASP 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 453 ILE Chi-restraints excluded: chain 3 residue 494 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 1 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 414 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 = 0.4250 r_free = 0.4250 target = 0.207201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124678 restraints weight = 10917.120| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.34 r_work: 0.3051 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 10962 Z= 0.376 Angle : 0.725 13.036 14979 Z= 0.378 Chirality : 0.051 0.273 1742 Planarity : 0.005 0.040 1958 Dihedral : 5.718 58.756 1646 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.93 % Allowed : 15.45 % Favored : 81.62 % 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: -0.88 (0.21), residues: 1483 helix: 1.32 (0.21), residues: 636 sheet: -1.33 (0.35), residues: 189 loop : -2.37 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP 2 291 HIS 0.009 0.002 HIS 3 485 PHE 0.026 0.003 PHE 2 38 TYR 0.024 0.003 TYR 3 171 ARG 0.005 0.001 ARG 2 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 2) link_NAG-ASN : angle 7.98954 ( 6) hydrogen bonds : bond 0.05730 ( 492) hydrogen bonds : angle 4.35462 ( 1431) SS BOND : bond 0.00400 ( 18) SS BOND : angle 1.28860 ( 36) covalent geometry : bond 0.00900 (10942) covalent geometry : angle 0.70571 (14937) *********************** 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 131 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.037 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7024 (ttm110) REVERT: 2 183 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8016 (ttm110) REVERT: 2 225 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: 2 226 LEU cc_start: 0.8511 (tt) cc_final: 0.7852 (mp) REVERT: 2 243 ARG cc_start: 0.7571 (mpt-90) cc_final: 0.6433 (mmp-170) REVERT: 2 373 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7857 (tp30) REVERT: 3 83 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7654 (p0) REVERT: 3 228 GLU cc_start: 0.8470 (tt0) cc_final: 0.8026 (tt0) REVERT: 3 360 GLN cc_start: 0.7490 (mt0) cc_final: 0.6949 (mm110) REVERT: 3 465 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.8100 (mtm180) REVERT: 3 493 ASP cc_start: 0.8080 (t0) cc_final: 0.7870 (t0) REVERT: 3 494 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7575 (t) REVERT: 3 508 GLN cc_start: 0.6940 (mt0) cc_final: 0.6349 (pt0) REVERT: 3 590 CYS cc_start: 0.7820 (m) cc_final: 0.7525 (t) outliers start: 29 outliers final: 19 residues processed: 129 average time/residue: 1.1832 time to fit residues: 165.5587 Evaluate side-chains 126 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 83 ARG Chi-restraints excluded: chain 2 residue 139 VAL 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 373 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 63 ASP Chi-restraints excluded: chain 3 residue 83 ASP 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 453 ILE Chi-restraints excluded: chain 3 residue 494 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 31 optimal weight: 0.0270 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 121 optimal weight: 0.0670 chunk 132 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 332 GLN 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.211304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134429 restraints weight = 10873.267| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.06 r_work: 0.3184 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3164 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= 0.126 Angle : 0.534 11.385 14979 Z= 0.277 Chirality : 0.042 0.273 1742 Planarity : 0.004 0.037 1958 Dihedral : 5.229 58.153 1646 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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 (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: -0.60 (0.22), residues: 1483 helix: 1.56 (0.21), residues: 654 sheet: -1.30 (0.35), residues: 189 loop : -2.30 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 291 HIS 0.005 0.001 HIS 3 485 PHE 0.013 0.001 PHE 2 623 TYR 0.014 0.001 TYR 3 186 ARG 0.003 0.000 ARG 3 68 Details of bonding type rmsd link_NAG-ASN : bond 0.01136 ( 2) link_NAG-ASN : angle 6.62269 ( 6) hydrogen bonds : bond 0.03912 ( 492) hydrogen bonds : angle 3.98812 ( 1431) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.78597 ( 36) covalent geometry : bond 0.00281 (10942) covalent geometry : angle 0.51707 (14937) ********************** 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 127 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.178 Fit side-chains REVERT: 2 83 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6948 (ttm110) REVERT: 2 183 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.7758 (ttm170) REVERT: 2 225 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: 2 226 LEU cc_start: 0.8345 (tt) cc_final: 0.7639 (mp) REVERT: 3 83 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7646 (p0) REVERT: 3 360 GLN cc_start: 0.7334 (mt0) cc_final: 0.6889 (mm110) REVERT: 3 465 ARG cc_start: 0.8383 (mtt-85) cc_final: 0.7959 (mtm180) REVERT: 3 493 ASP cc_start: 0.7853 (t0) cc_final: 0.7592 (t0) REVERT: 3 494 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7480 (t) REVERT: 3 590 CYS cc_start: 0.7795 (m) cc_final: 0.7446 (t) outliers start: 23 outliers final: 14 residues processed: 124 average time/residue: 1.1304 time to fit residues: 153.2978 Evaluate side-chains 120 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 426 VAL Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 63 ASP Chi-restraints excluded: chain 3 residue 83 ASP 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 453 ILE Chi-restraints excluded: chain 3 residue 494 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 13 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 332 GLN 3 414 ASN 3 473 ASN 3 485 HIS 3 495 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.210275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128710 restraints weight = 10836.887| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.15 r_work: 0.3156 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10962 Z= 0.175 Angle : 0.565 11.457 14979 Z= 0.293 Chirality : 0.043 0.267 1742 Planarity : 0.004 0.038 1958 Dihedral : 5.196 56.130 1646 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.12 % Allowed : 16.67 % Favored : 81.21 % 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: -0.53 (0.22), residues: 1483 helix: 1.60 (0.21), residues: 654 sheet: -1.11 (0.36), residues: 182 loop : -2.29 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 291 HIS 0.005 0.001 HIS 3 485 PHE 0.013 0.002 PHE 3 74 TYR 0.013 0.002 TYR 3 186 ARG 0.003 0.000 ARG 2 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00921 ( 2) link_NAG-ASN : angle 6.75528 ( 6) hydrogen bonds : bond 0.04271 ( 492) hydrogen bonds : angle 3.97657 ( 1431) SS BOND : bond 0.00193 ( 18) SS BOND : angle 0.81070 ( 36) covalent geometry : bond 0.00408 (10942) covalent geometry : angle 0.54770 (14937) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11207.41 seconds wall clock time: 201 minutes 42.64 seconds (12102.64 seconds total)