Starting phenix.real_space_refine on Mon Jul 28 23:46:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd4_36175/07_2025/8jd4_36175_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd4_36175/07_2025/8jd4_36175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd4_36175/07_2025/8jd4_36175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd4_36175/07_2025/8jd4_36175.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd4_36175/07_2025/8jd4_36175_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd4_36175/07_2025/8jd4_36175_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.071 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 69 5.16 5 C 6727 2.51 5 N 1872 2.21 5 O 2006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10674 Number of models: 1 Model: "" Number of chains: 5 Chain: "2" Number of atoms: 5241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5241 Classifications: {'peptide': 736} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 33, 'TRANS': 702} Chain breaks: 4 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 672 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 313 Chain: "4" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5371 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 35, 'TRANS': 720} Chain breaks: 6 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 10, 'GLU:plan': 9, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 339 Chain: "2" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "4" 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: 7.35, per 1000 atoms: 0.69 Number of scatterers: 10674 At special positions: 0 Unit cell: (98.532, 94.248, 182.07, 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 69 16.00 O 2006 8.00 N 1872 7.00 C 6727 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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=2.04 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 67 " - pdb=" SG CYS 4 109 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 249 " - pdb=" SG CYS 4 538 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 428 " - pdb=" SG CYS 4 435 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 520 " - pdb=" SG CYS 4 539 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 524 " - pdb=" SG CYS 4 542 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 545 " - pdb=" SG CYS 4 557 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 560 " - pdb=" SG CYS 4 573 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 652 " - pdb=" SG CYS 4 746 " 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 22001 " - " ASN 2 203 " " NAG 22002 " - " ASN 2 338 " " NAG 41102 " - " ASN 4 454 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2782 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 51.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain '2' and resid 58 through 75 Processing helix chain '2' and resid 94 through 106 Processing helix chain '2' and resid 144 through 159 removed outlier: 3.617A pdb=" N LEU 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 169 through 174 removed outlier: 3.515A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP 2 174 " --> pdb=" O LYS 2 171 " (cutoff:3.500A) Processing helix chain '2' and resid 187 through 202 removed outlier: 4.271A pdb=" N GLN 2 191 " --> pdb=" O PRO 2 187 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 231 removed outlier: 3.789A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG 2 231 " --> pdb=" O GLU 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 258 Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 324 through 333 removed outlier: 3.549A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 377 through 400 Processing helix chain '2' and resid 407 through 411 removed outlier: 3.810A pdb=" N ARG 2 411 " --> pdb=" O ASP 2 408 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 425 removed outlier: 4.046A pdb=" N LEU 2 424 " --> pdb=" O LYS 2 420 " (cutoff:3.500A) Processing helix chain '2' and resid 481 through 485 Processing helix chain '2' and resid 489 through 493 removed outlier: 3.956A pdb=" N GLY 2 493 " --> pdb=" O PRO 2 490 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 592 removed outlier: 3.869A pdb=" N THR 2 573 " --> pdb=" O VAL 2 569 " (cutoff:3.500A) Processing helix chain '2' and resid 603 through 626 removed outlier: 3.663A pdb=" N LEU 2 615 " --> pdb=" O GLY 2 611 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS 2 616 " --> pdb=" O GLY 2 612 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR 2 617 " --> pdb=" O VAL 2 613 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 2 620 " --> pdb=" O CYS 2 616 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS 2 626 " --> pdb=" O ILE 2 622 " (cutoff:3.500A) Processing helix chain '2' and resid 628 through 655 removed outlier: 3.665A pdb=" N THR 2 633 " --> pdb=" O THR 2 629 " (cutoff:3.500A) Processing helix chain '2' and resid 679 through 700 Processing helix chain '2' and resid 726 through 750 removed outlier: 4.259A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA 2 746 " --> pdb=" O CYS 2 742 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE 2 747 " --> pdb=" O THR 2 743 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 783 removed outlier: 3.549A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 786 through 809 removed outlier: 3.693A pdb=" N GLN 2 790 " --> pdb=" O ASP 2 786 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER 2 803 " --> pdb=" O SER 2 799 " (cutoff:3.500A) Processing helix chain '2' and resid 810 through 818 removed outlier: 3.607A pdb=" N ILE 2 816 " --> pdb=" O PRO 2 812 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE 2 817 " --> pdb=" O LYS 2 813 " (cutoff:3.500A) Processing helix chain '4' and resid 75 through 90 Processing helix chain '4' and resid 111 through 120 removed outlier: 3.581A pdb=" N LEU 4 116 " --> pdb=" O ASP 4 112 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 4 117 " --> pdb=" O THR 4 113 " (cutoff:3.500A) Processing helix chain '4' and resid 120 through 125 removed outlier: 4.731A pdb=" N ALA 4 125 " --> pdb=" O THR 4 121 " (cutoff:3.500A) Processing helix chain '4' and resid 158 through 170 removed outlier: 3.667A pdb=" N MET 4 164 " --> pdb=" O SER 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 171 through 173 No H-bonds generated for 'chain '4' and resid 171 through 173' Processing helix chain '4' and resid 183 through 188 Processing helix chain '4' and resid 201 through 216 Processing helix chain '4' and resid 230 through 246 Processing helix chain '4' and resid 263 through 275 removed outlier: 3.637A pdb=" N ILE 4 269 " --> pdb=" O PHE 4 265 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG 4 270 " --> pdb=" O ASP 4 266 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR 4 275 " --> pdb=" O ARG 4 271 " (cutoff:3.500A) Processing helix chain '4' and resid 286 through 300 Processing helix chain '4' and resid 312 through 315 removed outlier: 3.804A pdb=" N GLY 4 315 " --> pdb=" O ASP 4 312 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 312 through 315' Processing helix chain '4' and resid 341 through 350 removed outlier: 3.578A pdb=" N ASP 4 345 " --> pdb=" O VAL 4 341 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG 4 346 " --> pdb=" O ARG 4 342 " (cutoff:3.500A) Processing helix chain '4' and resid 361 through 371 removed outlier: 4.074A pdb=" N GLU 4 367 " --> pdb=" O ALA 4 363 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP 4 368 " --> pdb=" O GLU 4 364 " (cutoff:3.500A) Processing helix chain '4' and resid 393 through 398 removed outlier: 3.630A pdb=" N SER 4 398 " --> pdb=" O ILE 4 394 " (cutoff:3.500A) Processing helix chain '4' and resid 405 through 428 removed outlier: 3.871A pdb=" N ASP 4 426 " --> pdb=" O ALA 4 422 " (cutoff:3.500A) Processing helix chain '4' and resid 442 through 451 removed outlier: 3.634A pdb=" N LYS 4 448 " --> pdb=" O THR 4 444 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR 4 449 " --> pdb=" O GLN 4 445 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 461 removed outlier: 3.945A pdb=" N ASN 4 461 " --> pdb=" O ILE 4 458 " (cutoff:3.500A) Processing helix chain '4' and resid 502 through 506 Processing helix chain '4' and resid 588 through 612 removed outlier: 3.676A pdb=" N LEU 4 592 " --> pdb=" O ALA 4 588 " (cutoff:3.500A) Processing helix chain '4' and resid 614 through 622 removed outlier: 3.671A pdb=" N ALA 4 620 " --> pdb=" O PRO 4 616 " (cutoff:3.500A) Processing helix chain '4' and resid 624 through 644 removed outlier: 3.599A pdb=" N VAL 4 628 " --> pdb=" O GLU 4 624 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE 4 641 " --> pdb=" O TYR 4 637 " (cutoff:3.500A) Processing helix chain '4' and resid 648 through 654 Processing helix chain '4' and resid 654 through 682 Processing helix chain '4' and resid 695 through 721 removed outlier: 4.208A pdb=" N ASP 4 721 " --> pdb=" O TRP 4 717 " (cutoff:3.500A) Processing helix chain '4' and resid 749 through 775 removed outlier: 3.501A pdb=" N SER 4 760 " --> pdb=" O LEU 4 756 " (cutoff:3.500A) Processing helix chain '4' and resid 781 through 800 Proline residue: 4 786 - end of helix Processing helix chain '4' and resid 800 through 808 removed outlier: 3.750A pdb=" N ILE 4 804 " --> pdb=" O ALA 4 800 " (cutoff:3.500A) Processing helix chain '4' and resid 814 through 848 removed outlier: 3.727A pdb=" N THR 4 820 " --> pdb=" O TYR 4 816 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 4 837 " --> pdb=" O SER 4 833 " (cutoff:3.500A) Proline residue: 4 840 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 25 through 28 removed outlier: 6.968A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain '2' and resid 235 through 241 removed outlier: 7.725A pdb=" N VAL 2 207 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER 2 238 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR 2 209 " --> pdb=" O SER 2 238 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS 2 240 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA 2 211 " --> pdb=" O LYS 2 240 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N PHE 2 269 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL 2 210 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA 2 266 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 428 through 429 removed outlier: 3.968A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 510 through 511 Processing sheet with id=AA6, first strand: chain '4' and resid 43 through 45 removed outlier: 6.381A pdb=" N ILE 4 49 " --> pdb=" O GLY 4 102 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ARG 4 104 " --> pdb=" O ILE 4 49 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU 4 51 " --> pdb=" O ARG 4 104 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU 4 106 " --> pdb=" O LEU 4 51 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY 4 53 " --> pdb=" O LEU 4 106 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR 4 50 " --> pdb=" O VAL 4 150 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY 4 152 " --> pdb=" O THR 4 50 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN 4 176 " --> pdb=" O SER 4 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '4' and resid 58 through 60 removed outlier: 4.303A pdb=" N GLU 4 69 " --> pdb=" O GLY 4 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '4' and resid 249 through 256 removed outlier: 7.667A pdb=" N VAL 4 221 " --> pdb=" O GLN 4 252 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N VAL 4 254 " --> pdb=" O VAL 4 221 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR 4 223 " --> pdb=" O VAL 4 254 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE 4 256 " --> pdb=" O THR 4 223 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA 4 225 " --> pdb=" O ILE 4 256 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR 4 220 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE 4 282 " --> pdb=" O TYR 4 220 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER 4 222 " --> pdb=" O ILE 4 282 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TRP 4 308 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE 4 334 " --> pdb=" O TRP 4 308 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY 4 310 " --> pdb=" O ILE 4 334 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY 4 493 " --> pdb=" O ILE 4 477 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLN 4 479 " --> pdb=" O VAL 4 491 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL 4 491 " --> pdb=" O GLN 4 479 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN 4 481 " --> pdb=" O TYR 4 489 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR 4 489 " --> pdb=" O GLN 4 481 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '4' and resid 529 through 533 Processing sheet with id=AB1, first strand: chain '4' and resid 549 through 550 Processing sheet with id=AB2, first strand: chain '4' and resid 564 through 566 553 hydrogen bonds defined for protein. 1614 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: 4.16 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3577 1.34 - 1.46: 2571 1.46 - 1.59: 4655 1.59 - 1.71: 0 1.71 - 1.83: 91 Bond restraints: 10894 Sorted by residual: bond pdb=" N ILE 4 578 " pdb=" CA ILE 4 578 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.08e-02 8.57e+03 1.20e+01 bond pdb=" N VAL 2 207 " pdb=" CA VAL 2 207 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.14e+01 bond pdb=" N TRP 2 520 " pdb=" CA TRP 2 520 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.25e-02 6.40e+03 8.17e+00 bond pdb=" N ARG 2 499 " pdb=" CA ARG 2 499 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.12e+00 bond pdb=" N CYS 2 518 " pdb=" CA CYS 2 518 " ideal model delta sigma weight residual 1.460 1.489 -0.029 1.02e-02 9.61e+03 8.05e+00 ... (remaining 10889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 14425 1.34 - 2.68: 334 2.68 - 4.02: 87 4.02 - 5.36: 24 5.36 - 6.70: 4 Bond angle restraints: 14874 Sorted by residual: angle pdb=" N ARG 4 741 " pdb=" CA ARG 4 741 " pdb=" C ARG 4 741 " ideal model delta sigma weight residual 114.09 108.39 5.70 1.55e+00 4.16e-01 1.35e+01 angle pdb=" C CYS 2 518 " pdb=" CA CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sigma weight residual 114.87 109.70 5.17 1.51e+00 4.39e-01 1.17e+01 angle pdb=" N ASP 4 563 " pdb=" CA ASP 4 563 " pdb=" C ASP 4 563 " ideal model delta sigma weight residual 113.02 108.96 4.06 1.20e+00 6.94e-01 1.15e+01 angle pdb=" CA ILE 4 578 " pdb=" C ILE 4 578 " pdb=" O ILE 4 578 " ideal model delta sigma weight residual 121.45 118.14 3.31 1.00e+00 1.00e+00 1.09e+01 angle pdb=" CA PRO 4 803 " pdb=" N PRO 4 803 " pdb=" CD PRO 4 803 " ideal model delta sigma weight residual 112.00 107.39 4.61 1.40e+00 5.10e-01 1.09e+01 ... (remaining 14869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 6195 23.07 - 46.14: 268 46.14 - 69.21: 33 69.21 - 92.28: 9 92.28 - 115.35: 8 Dihedral angle restraints: 6513 sinusoidal: 2213 harmonic: 4300 Sorted by residual: dihedral pdb=" CB CYS 2 50 " pdb=" SG CYS 2 50 " pdb=" SG CYS 2 92 " pdb=" CB CYS 2 92 " ideal model delta sinusoidal sigma weight residual -86.00 3.08 -89.08 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CB CYS 2 540 " pdb=" SG CYS 2 540 " pdb=" SG CYS 2 553 " pdb=" CB CYS 2 553 " ideal model delta sinusoidal sigma weight residual 93.00 -178.55 -88.45 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS 4 67 " pdb=" SG CYS 4 67 " pdb=" SG CYS 4 109 " pdb=" CB CYS 4 109 " ideal model delta sinusoidal sigma weight residual -86.00 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1558 0.066 - 0.132: 164 0.132 - 0.199: 13 0.199 - 0.265: 1 0.265 - 0.331: 1 Chirality restraints: 1737 Sorted by residual: chirality pdb=" C1 NAG 22001 " pdb=" ND2 ASN 2 203 " pdb=" C2 NAG 22001 " pdb=" O5 NAG 22001 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG 22002 " pdb=" ND2 ASN 2 338 " pdb=" C2 NAG 22002 " pdb=" O5 NAG 22002 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE 4 576 " pdb=" N ILE 4 576 " pdb=" C ILE 4 576 " pdb=" CB ILE 4 576 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 1734 not shown) Planarity restraints: 1947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 2 411 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO 2 412 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE 4 802 " -0.047 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO 4 803 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO 4 803 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 4 803 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP 2 545 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO 2 546 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 2 546 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO 2 546 " 0.031 5.00e-02 4.00e+02 ... (remaining 1944 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3024 2.81 - 3.33: 10430 3.33 - 3.86: 17520 3.86 - 4.38: 20002 4.38 - 4.90: 34140 Nonbonded interactions: 85116 Sorted by model distance: nonbonded pdb=" N TYR 2 530 " pdb=" O ALA 2 538 " model vdw 2.289 3.120 nonbonded pdb=" NE2 HIS 4 424 " pdb=" O GLY 4 433 " model vdw 2.310 3.120 nonbonded pdb=" NH1 ARG 2 452 " pdb=" O TYR 2 453 " model vdw 2.314 3.120 nonbonded pdb=" O ILE 2 324 " pdb=" NE2 GLN 2 374 " model vdw 2.314 3.120 nonbonded pdb=" NH2 ARG 2 264 " pdb=" O SER 2 288 " model vdw 2.331 3.120 ... (remaining 85111 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: 0.010 Normalize map: mean=0, sd=1: 5.490 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.880 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:18.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.003 0.068 10914 Z= 0.183 Angle : 0.542 12.059 14917 Z= 0.300 Chirality : 0.042 0.331 1737 Planarity : 0.004 0.072 1944 Dihedral : 13.243 115.350 3680 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.20 % Allowed : 0.30 % Favored : 99.49 % 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: -0.19 (0.22), residues: 1468 helix: 1.20 (0.20), residues: 686 sheet: -0.64 (0.44), residues: 148 loop : -1.51 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 4 218 HIS 0.001 0.000 HIS 4 507 PHE 0.010 0.001 PHE 2 189 TYR 0.016 0.001 TYR 2 458 ARG 0.002 0.000 ARG 2 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 3) link_NAG-ASN : angle 5.09251 ( 9) hydrogen bonds : bond 0.24394 ( 553) hydrogen bonds : angle 7.17175 ( 1614) SS BOND : bond 0.00235 ( 17) SS BOND : angle 1.14146 ( 34) covalent geometry : bond 0.00296 (10894) covalent geometry : angle 0.52578 (14874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.971 Fit side-chains REVERT: 2 94 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7971 (mttt) REVERT: 2 2003 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8644 (pm20) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 1.3613 time to fit residues: 196.5259 Evaluate side-chains 99 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 2003 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 283 GLN 4 402 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.192867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132775 restraints weight = 13662.395| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.32 r_work: 0.3242 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10914 Z= 0.212 Angle : 0.652 10.408 14917 Z= 0.336 Chirality : 0.046 0.369 1737 Planarity : 0.005 0.049 1944 Dihedral : 6.408 59.200 1655 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.89 % Rotamer: Outliers : 2.63 % Allowed : 8.71 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1468 helix: 1.49 (0.19), residues: 695 sheet: -0.80 (0.40), residues: 163 loop : -1.43 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 4 218 HIS 0.003 0.001 HIS 4 498 PHE 0.031 0.002 PHE 2 422 TYR 0.016 0.002 TYR 4 220 ARG 0.006 0.001 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 3) link_NAG-ASN : angle 4.44196 ( 9) hydrogen bonds : bond 0.05779 ( 553) hydrogen bonds : angle 4.86662 ( 1614) SS BOND : bond 0.00356 ( 17) SS BOND : angle 1.34365 ( 34) covalent geometry : bond 0.00496 (10894) covalent geometry : angle 0.64008 (14874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.943 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7690 (mpt90) REVERT: 4 164 MET cc_start: 0.8623 (mtt) cc_final: 0.8405 (mtt) REVERT: 4 267 LYS cc_start: 0.8206 (tmtm) cc_final: 0.7778 (ttmm) REVERT: 4 309 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8704 (ttm) REVERT: 4 438 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.5597 (ttt) REVERT: 4 564 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7301 (mpt) outliers start: 26 outliers final: 6 residues processed: 120 average time/residue: 1.6469 time to fit residues: 215.5788 Evaluate side-chains 97 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 411 ARG Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 309 MET Chi-restraints excluded: chain 4 residue 337 LYS Chi-restraints excluded: chain 4 residue 438 MET Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 564 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 359 ASN 4 507 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.190555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121449 restraints weight = 13722.580| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.35 r_work: 0.3065 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10914 Z= 0.165 Angle : 0.584 9.466 14917 Z= 0.297 Chirality : 0.044 0.319 1737 Planarity : 0.004 0.045 1944 Dihedral : 5.002 52.317 1652 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.33 % Allowed : 12.26 % Favored : 85.41 % 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: 0.17 (0.22), residues: 1468 helix: 1.65 (0.19), residues: 692 sheet: -0.84 (0.40), residues: 166 loop : -1.46 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 4 218 HIS 0.009 0.001 HIS 4 507 PHE 0.026 0.001 PHE 2 422 TYR 0.012 0.002 TYR 4 179 ARG 0.004 0.000 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 3) link_NAG-ASN : angle 3.64329 ( 9) hydrogen bonds : bond 0.05094 ( 553) hydrogen bonds : angle 4.56887 ( 1614) SS BOND : bond 0.00257 ( 17) SS BOND : angle 1.12134 ( 34) covalent geometry : bond 0.00382 (10894) covalent geometry : angle 0.57584 (14874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.107 Fit side-chains REVERT: 4 164 MET cc_start: 0.8660 (mtt) cc_final: 0.8437 (mtt) REVERT: 4 267 LYS cc_start: 0.8189 (tmtm) cc_final: 0.7847 (ttmm) REVERT: 4 309 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8653 (ttm) REVERT: 4 564 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7395 (mpt) REVERT: 4 643 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6941 (mmp) outliers start: 23 outliers final: 10 residues processed: 104 average time/residue: 1.0903 time to fit residues: 123.7902 Evaluate side-chains 96 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 2 residue 424 LEU Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 770 CYS Chi-restraints excluded: chain 4 residue 309 MET Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 564 MET Chi-restraints excluded: chain 4 residue 643 MET Chi-restraints excluded: chain 4 residue 808 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 58 optimal weight: 50.0000 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.191324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121436 restraints weight = 13652.814| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.32 r_work: 0.3099 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10914 Z= 0.133 Angle : 0.549 8.414 14917 Z= 0.277 Chirality : 0.042 0.295 1737 Planarity : 0.004 0.042 1944 Dihedral : 4.685 47.219 1652 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.63 % Allowed : 13.98 % Favored : 83.38 % 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: 0.27 (0.22), residues: 1468 helix: 1.70 (0.19), residues: 702 sheet: -0.82 (0.40), residues: 166 loop : -1.40 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 4 218 HIS 0.002 0.000 HIS 2 390 PHE 0.024 0.001 PHE 2 422 TYR 0.014 0.001 TYR 4 220 ARG 0.002 0.000 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 3) link_NAG-ASN : angle 3.20240 ( 9) hydrogen bonds : bond 0.04469 ( 553) hydrogen bonds : angle 4.34321 ( 1614) SS BOND : bond 0.00257 ( 17) SS BOND : angle 1.24046 ( 34) covalent geometry : bond 0.00300 (10894) covalent geometry : angle 0.54060 (14874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.062 Fit side-chains REVERT: 4 564 MET cc_start: 0.7815 (mmm) cc_final: 0.7349 (mpt) REVERT: 4 837 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (pp) REVERT: 4 1101 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8719 (pt0) outliers start: 26 outliers final: 10 residues processed: 107 average time/residue: 0.9702 time to fit residues: 114.6788 Evaluate side-chains 97 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 808 THR Chi-restraints excluded: chain 4 residue 837 LEU Chi-restraints excluded: chain 4 residue 1101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 46 optimal weight: 0.0270 chunk 44 optimal weight: 0.0010 chunk 53 optimal weight: 30.0000 chunk 117 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 overall best weight: 0.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.192079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124570 restraints weight = 13630.731| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.34 r_work: 0.3122 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10914 Z= 0.115 Angle : 0.533 9.137 14917 Z= 0.267 Chirality : 0.041 0.270 1737 Planarity : 0.003 0.040 1944 Dihedral : 4.355 42.869 1652 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.13 % Allowed : 15.70 % Favored : 82.17 % 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: 0.37 (0.22), residues: 1468 helix: 1.79 (0.19), residues: 704 sheet: -0.83 (0.41), residues: 166 loop : -1.35 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 218 HIS 0.002 0.000 HIS 4 507 PHE 0.023 0.001 PHE 2 422 TYR 0.012 0.001 TYR 4 612 ARG 0.002 0.000 ARG 2 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 3) link_NAG-ASN : angle 2.63516 ( 9) hydrogen bonds : bond 0.04151 ( 553) hydrogen bonds : angle 4.18159 ( 1614) SS BOND : bond 0.00243 ( 17) SS BOND : angle 1.07129 ( 34) covalent geometry : bond 0.00250 (10894) covalent geometry : angle 0.52723 (14874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.238 Fit side-chains REVERT: 4 219 ASN cc_start: 0.7698 (m-40) cc_final: 0.7348 (p0) REVERT: 4 564 MET cc_start: 0.7877 (mmm) cc_final: 0.7426 (mpt) REVERT: 4 837 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8250 (pp) outliers start: 21 outliers final: 7 residues processed: 111 average time/residue: 1.1892 time to fit residues: 147.0800 Evaluate side-chains 98 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.188571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114094 restraints weight = 13635.164| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.98 r_work: 0.3065 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10914 Z= 0.214 Angle : 0.626 9.030 14917 Z= 0.319 Chirality : 0.045 0.256 1737 Planarity : 0.005 0.052 1944 Dihedral : 4.872 51.782 1652 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 2.43 % Allowed : 16.62 % Favored : 80.95 % 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: 0.27 (0.22), residues: 1468 helix: 1.83 (0.19), residues: 694 sheet: -0.96 (0.41), residues: 168 loop : -1.49 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 218 HIS 0.003 0.001 HIS 2 97 PHE 0.028 0.002 PHE 2 422 TYR 0.015 0.002 TYR 4 179 ARG 0.004 0.001 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 3) link_NAG-ASN : angle 2.64648 ( 9) hydrogen bonds : bond 0.04843 ( 553) hydrogen bonds : angle 4.32686 ( 1614) SS BOND : bond 0.00298 ( 17) SS BOND : angle 1.62691 ( 34) covalent geometry : bond 0.00510 (10894) covalent geometry : angle 0.61910 (14874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.688 Fit side-chains REVERT: 2 312 GLU cc_start: 0.8316 (tp30) cc_final: 0.8033 (mt-10) REVERT: 2 411 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7671 (mpt90) REVERT: 4 564 MET cc_start: 0.7770 (mmm) cc_final: 0.7343 (mpt) REVERT: 4 817 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8544 (tp) REVERT: 4 837 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8271 (pp) outliers start: 24 outliers final: 12 residues processed: 108 average time/residue: 1.2131 time to fit residues: 144.0530 Evaluate side-chains 101 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 411 ARG Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 108 THR Chi-restraints excluded: chain 4 residue 119 SER Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 337 LYS Chi-restraints excluded: chain 4 residue 428 CYS Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 817 ILE Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 30.0000 chunk 13 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 122 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 40.0000 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 414 ASN 4 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.190741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124555 restraints weight = 13820.458| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.23 r_work: 0.3103 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10914 Z= 0.128 Angle : 0.554 9.946 14917 Z= 0.279 Chirality : 0.042 0.250 1737 Planarity : 0.004 0.037 1944 Dihedral : 4.514 47.530 1652 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 1.93 % Allowed : 17.63 % Favored : 80.45 % 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: 1468 helix: 1.88 (0.19), residues: 701 sheet: -0.94 (0.40), residues: 168 loop : -1.41 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 218 HIS 0.003 0.001 HIS 4 507 PHE 0.024 0.001 PHE 2 422 TYR 0.012 0.001 TYR 4 612 ARG 0.003 0.000 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 3) link_NAG-ASN : angle 2.40247 ( 9) hydrogen bonds : bond 0.04192 ( 553) hydrogen bonds : angle 4.14576 ( 1614) SS BOND : bond 0.00226 ( 17) SS BOND : angle 1.14478 ( 34) covalent geometry : bond 0.00287 (10894) covalent geometry : angle 0.54899 (14874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.452 Fit side-chains REVERT: 2 247 ARG cc_start: 0.7835 (ptp-170) cc_final: 0.7495 (mtm180) REVERT: 4 267 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7571 (tppt) REVERT: 4 564 MET cc_start: 0.7789 (mmm) cc_final: 0.7425 (mpt) REVERT: 4 837 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8255 (pp) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 1.3444 time to fit residues: 154.6138 Evaluate side-chains 96 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 119 SER Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 428 CYS Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 0.2980 chunk 47 optimal weight: 9.9990 chunk 129 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 144 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.190498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121924 restraints weight = 13612.313| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.22 r_work: 0.3075 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10914 Z= 0.137 Angle : 0.553 9.863 14917 Z= 0.278 Chirality : 0.042 0.233 1737 Planarity : 0.004 0.035 1944 Dihedral : 4.473 46.982 1652 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 1.93 % Allowed : 17.93 % Favored : 80.14 % 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: 0.43 (0.22), residues: 1468 helix: 1.95 (0.19), residues: 701 sheet: -0.97 (0.40), residues: 168 loop : -1.41 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 4 218 HIS 0.003 0.001 HIS 4 507 PHE 0.024 0.001 PHE 2 422 TYR 0.011 0.001 TYR 4 612 ARG 0.002 0.000 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 3) link_NAG-ASN : angle 2.21466 ( 9) hydrogen bonds : bond 0.04167 ( 553) hydrogen bonds : angle 4.09592 ( 1614) SS BOND : bond 0.00237 ( 17) SS BOND : angle 1.02652 ( 34) covalent geometry : bond 0.00315 (10894) covalent geometry : angle 0.54850 (14874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 1.155 Fit side-chains REVERT: 2 247 ARG cc_start: 0.7669 (ptp-170) cc_final: 0.7335 (mtm180) REVERT: 2 619 MET cc_start: 0.6961 (ptm) cc_final: 0.6711 (ptp) REVERT: 4 403 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7920 (tp30) REVERT: 4 506 MET cc_start: 0.8461 (mtm) cc_final: 0.8116 (mtm) REVERT: 4 837 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8260 (pp) outliers start: 19 outliers final: 14 residues processed: 100 average time/residue: 1.4792 time to fit residues: 163.3386 Evaluate side-chains 98 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 108 THR Chi-restraints excluded: chain 4 residue 119 SER Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 403 GLU Chi-restraints excluded: chain 4 residue 428 CYS Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.190354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118288 restraints weight = 13782.411| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.21 r_work: 0.3074 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10914 Z= 0.137 Angle : 0.558 10.374 14917 Z= 0.280 Chirality : 0.042 0.227 1737 Planarity : 0.004 0.035 1944 Dihedral : 4.456 47.129 1652 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 2.03 % Allowed : 17.73 % Favored : 80.24 % 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: 0.47 (0.22), residues: 1468 helix: 2.00 (0.19), residues: 701 sheet: -0.96 (0.40), residues: 168 loop : -1.41 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 4 218 HIS 0.003 0.001 HIS 4 507 PHE 0.024 0.001 PHE 2 422 TYR 0.011 0.001 TYR 4 612 ARG 0.002 0.000 ARG 2 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 3) link_NAG-ASN : angle 2.11871 ( 9) hydrogen bonds : bond 0.04121 ( 553) hydrogen bonds : angle 4.04892 ( 1614) SS BOND : bond 0.00241 ( 17) SS BOND : angle 0.95116 ( 34) covalent geometry : bond 0.00318 (10894) covalent geometry : angle 0.55406 (14874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 2.101 Fit side-chains REVERT: 2 247 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.7328 (mtm180) REVERT: 2 619 MET cc_start: 0.6927 (ptm) cc_final: 0.6656 (ptp) REVERT: 4 267 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7651 (tppt) REVERT: 4 403 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: 4 817 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8474 (tp) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 1.6212 time to fit residues: 186.8532 Evaluate side-chains 100 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 108 THR Chi-restraints excluded: chain 4 residue 119 SER Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 403 GLU Chi-restraints excluded: chain 4 residue 428 CYS Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 817 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 507 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.188630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119088 restraints weight = 13716.155| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.35 r_work: 0.3052 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10914 Z= 0.194 Angle : 0.611 11.136 14917 Z= 0.310 Chirality : 0.044 0.219 1737 Planarity : 0.004 0.039 1944 Dihedral : 4.757 52.238 1652 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 2.03 % Allowed : 17.93 % Favored : 80.04 % 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: 1468 helix: 1.95 (0.19), residues: 699 sheet: -1.09 (0.40), residues: 170 loop : -1.50 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 218 HIS 0.010 0.001 HIS 4 507 PHE 0.024 0.002 PHE 2 422 TYR 0.014 0.002 TYR 4 179 ARG 0.003 0.000 ARG 4 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 3) link_NAG-ASN : angle 2.27683 ( 9) hydrogen bonds : bond 0.04545 ( 553) hydrogen bonds : angle 4.17184 ( 1614) SS BOND : bond 0.00261 ( 17) SS BOND : angle 1.06491 ( 34) covalent geometry : bond 0.00465 (10894) covalent geometry : angle 0.60765 (14874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 1.100 Fit side-chains REVERT: 2 247 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7472 (mtm180) REVERT: 2 312 GLU cc_start: 0.8353 (tp30) cc_final: 0.8039 (mt-10) REVERT: 2 619 MET cc_start: 0.6981 (ptm) cc_final: 0.6704 (ptp) REVERT: 4 403 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: 4 817 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8492 (tp) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.9680 time to fit residues: 106.0318 Evaluate side-chains 100 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 2 residue 770 CYS Chi-restraints excluded: chain 2 residue 779 ILE Chi-restraints excluded: chain 4 residue 108 THR Chi-restraints excluded: chain 4 residue 119 SER Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 403 GLU Chi-restraints excluded: chain 4 residue 428 CYS Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 817 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 11 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 359 ASN 4 507 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117526 restraints weight = 13508.512| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.26 r_work: 0.3055 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10914 Z= 0.141 Angle : 0.569 10.911 14917 Z= 0.286 Chirality : 0.042 0.216 1737 Planarity : 0.004 0.034 1944 Dihedral : 4.575 49.170 1652 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 1.93 % Allowed : 18.14 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.22), residues: 1468 helix: 2.00 (0.19), residues: 701 sheet: -1.09 (0.40), residues: 170 loop : -1.45 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 4 218 HIS 0.009 0.001 HIS 4 507 PHE 0.022 0.001 PHE 2 422 TYR 0.011 0.001 TYR 4 612 ARG 0.003 0.000 ARG 4 197 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 3) link_NAG-ASN : angle 2.08660 ( 9) hydrogen bonds : bond 0.04105 ( 553) hydrogen bonds : angle 4.06625 ( 1614) SS BOND : bond 0.00266 ( 17) SS BOND : angle 0.95426 ( 34) covalent geometry : bond 0.00325 (10894) covalent geometry : angle 0.56549 (14874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9299.74 seconds wall clock time: 171 minutes 52.38 seconds (10312.38 seconds total)