Starting phenix.real_space_refine on Sat Oct 11 02:11:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd4_36175/10_2025/8jd4_36175_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd4_36175/10_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_36175/10_2025/8jd4_36175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd4_36175/10_2025/8jd4_36175.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd4_36175/10_2025/8jd4_36175_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd4_36175/10_2025/8jd4_36175_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 12, 'ARG:plan': 16, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 5, 'TYR:plan': 8, 'PHE:plan': 8, 'HIS:plan': 2, 'TRP:plan': 2} 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: {'GLU:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 18, 'GLN:plan1': 8, 'TRP:plan': 2, 'TYR:plan': 9, 'ASP:plan': 8, 'PHE:plan': 10, 'HIS:plan': 2} 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: 2.95, per 1000 atoms: 0.28 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: 0.76 Conformation dependent library (CDL) restraints added in 531.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.40 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: 1.97 Time building geometry restraints manager: 1.04 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: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (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 ARG 0.002 0.000 ARG 2 452 TYR 0.016 0.001 TYR 2 458 PHE 0.010 0.001 PHE 2 189 TRP 0.019 0.001 TRP 4 218 HIS 0.001 0.000 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00296 (10894) covalent geometry : angle 0.52578 (14874) SS BOND : bond 0.00235 ( 17) SS BOND : angle 1.14146 ( 34) hydrogen bonds : bond 0.24394 ( 553) hydrogen bonds : angle 7.17175 ( 1614) link_NAG-ASN : bond 0.00864 ( 3) link_NAG-ASN : angle 5.09251 ( 9) *********************** 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 : 0.434 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: 0.5778 time to fit residues: 83.0237 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 : 0.404 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0870 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 9.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.194148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126419 restraints weight = 13900.991| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.19 r_work: 0.3174 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1788 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= 0.161 Angle : 0.593 10.215 14917 Z= 0.304 Chirality : 0.044 0.349 1737 Planarity : 0.004 0.050 1944 Dihedral : 6.444 62.462 1655 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.57 % Rotamer: Outliers : 2.23 % Allowed : 8.41 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1468 helix: 1.52 (0.19), residues: 704 sheet: -0.68 (0.41), residues: 164 loop : -1.36 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 61 TYR 0.015 0.002 TYR 4 612 PHE 0.027 0.002 PHE 2 422 TRP 0.024 0.001 TRP 4 218 HIS 0.003 0.001 HIS 4 498 Details of bonding type rmsd covalent geometry : bond 0.00360 (10894) covalent geometry : angle 0.58116 (14874) SS BOND : bond 0.00299 ( 17) SS BOND : angle 1.29861 ( 34) hydrogen bonds : bond 0.05655 ( 553) hydrogen bonds : angle 4.84557 ( 1614) link_NAG-ASN : bond 0.00750 ( 3) link_NAG-ASN : angle 4.31090 ( 9) *********************** 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 125 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.410 Fit side-chains REVERT: 2 411 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7730 (mpt90) REVERT: 4 44 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7032 (mtt90) REVERT: 4 267 LYS cc_start: 0.8073 (tmtm) cc_final: 0.7762 (ttmm) REVERT: 4 309 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8560 (ttm) REVERT: 4 564 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7464 (mpp) outliers start: 22 outliers final: 5 residues processed: 114 average time/residue: 0.5436 time to fit residues: 67.5342 Evaluate side-chains 100 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 2 residue 424 LEU Chi-restraints excluded: chain 4 residue 44 ARG Chi-restraints excluded: chain 4 residue 309 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 15 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 50.0000 chunk 90 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 305 HIS 4 359 ASN 4 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.186282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112728 restraints weight = 13558.320| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.23 r_work: 0.2969 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.083 10914 Z= 0.401 Angle : 0.791 12.270 14917 Z= 0.409 Chirality : 0.054 0.372 1737 Planarity : 0.007 0.101 1944 Dihedral : 6.034 62.465 1652 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 3.75 % Allowed : 11.75 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.21), residues: 1468 helix: 1.40 (0.19), residues: 684 sheet: -1.03 (0.40), residues: 171 loop : -1.73 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 61 TYR 0.026 0.003 TYR 4 179 PHE 0.036 0.003 PHE 2 422 TRP 0.046 0.003 TRP 4 218 HIS 0.007 0.002 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00965 (10894) covalent geometry : angle 0.78117 (14874) SS BOND : bond 0.00471 ( 17) SS BOND : angle 1.36703 ( 34) hydrogen bonds : bond 0.06516 ( 553) hydrogen bonds : angle 4.93204 ( 1614) link_NAG-ASN : bond 0.00362 ( 3) link_NAG-ASN : angle 4.70862 ( 9) *********************** 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 131 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.416 Fit side-chains REVERT: 2 290 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7568 (m) REVERT: 2 411 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7633 (mpt90) REVERT: 4 243 ARG cc_start: 0.7327 (tpp80) cc_final: 0.7096 (ttp-110) REVERT: 4 267 LYS cc_start: 0.8306 (tmtm) cc_final: 0.7864 (ttmm) REVERT: 4 309 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8796 (ttm) REVERT: 4 437 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7794 (ptt180) REVERT: 4 438 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5516 (ttt) REVERT: 4 564 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7289 (mpt) REVERT: 4 643 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.7024 (mmp) outliers start: 37 outliers final: 14 residues processed: 118 average time/residue: 0.6249 time to fit residues: 79.5340 Evaluate side-chains 106 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 411 ARG Chi-restraints excluded: chain 2 residue 417 ARG Chi-restraints excluded: chain 2 residue 426 VAL 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 153 VAL Chi-restraints excluded: chain 4 residue 309 MET Chi-restraints excluded: chain 4 residue 337 LYS Chi-restraints excluded: chain 4 residue 437 ARG Chi-restraints excluded: chain 4 residue 438 MET Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 564 MET Chi-restraints excluded: chain 4 residue 567 THR Chi-restraints excluded: chain 4 residue 643 MET Chi-restraints excluded: chain 4 residue 808 THR Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 127 optimal weight: 30.0000 chunk 129 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.189077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.123199 restraints weight = 13788.896| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.26 r_work: 0.3049 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10914 Z= 0.166 Angle : 0.594 8.515 14917 Z= 0.304 Chirality : 0.044 0.307 1737 Planarity : 0.004 0.058 1944 Dihedral : 5.311 56.032 1652 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 3.04 % Allowed : 14.39 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1468 helix: 1.56 (0.19), residues: 693 sheet: -1.13 (0.39), residues: 167 loop : -1.59 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 61 TYR 0.020 0.002 TYR 4 220 PHE 0.028 0.001 PHE 2 422 TRP 0.025 0.001 TRP 4 218 HIS 0.006 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00386 (10894) covalent geometry : angle 0.58412 (14874) SS BOND : bond 0.00306 ( 17) SS BOND : angle 1.42639 ( 34) hydrogen bonds : bond 0.04942 ( 553) hydrogen bonds : angle 4.57861 ( 1614) link_NAG-ASN : bond 0.00522 ( 3) link_NAG-ASN : angle 3.67451 ( 9) *********************** 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 121 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.420 Fit side-chains REVERT: 2 411 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7588 (mpt90) REVERT: 4 267 LYS cc_start: 0.8239 (tmtm) cc_final: 0.7885 (ttmm) REVERT: 4 309 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8622 (ttm) REVERT: 4 564 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7326 (mpt) outliers start: 30 outliers final: 11 residues processed: 112 average time/residue: 0.5634 time to fit residues: 68.5320 Evaluate side-chains 96 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 227 GLU 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 411 ARG Chi-restraints excluded: chain 2 residue 509 VAL Chi-restraints excluded: chain 4 residue 108 THR 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 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 564 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 4 507 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.190116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117097 restraints weight = 13559.461| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.04 r_work: 0.3110 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10914 Z= 0.136 Angle : 0.566 8.925 14917 Z= 0.286 Chirality : 0.042 0.286 1737 Planarity : 0.004 0.061 1944 Dihedral : 4.858 50.107 1652 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 3.04 % Allowed : 15.60 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.22), residues: 1468 helix: 1.70 (0.20), residues: 698 sheet: -1.05 (0.39), residues: 168 loop : -1.56 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 61 TYR 0.013 0.001 TYR 4 612 PHE 0.023 0.001 PHE 2 422 TRP 0.015 0.001 TRP 4 218 HIS 0.010 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00307 (10894) covalent geometry : angle 0.55879 (14874) SS BOND : bond 0.00223 ( 17) SS BOND : angle 1.12786 ( 34) hydrogen bonds : bond 0.04498 ( 553) hydrogen bonds : angle 4.35637 ( 1614) link_NAG-ASN : bond 0.00489 ( 3) link_NAG-ASN : angle 3.11225 ( 9) *********************** 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 115 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: 4 403 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: 4 564 MET cc_start: 0.7909 (mmm) cc_final: 0.7376 (mpt) outliers start: 30 outliers final: 13 residues processed: 105 average time/residue: 0.5057 time to fit residues: 58.2350 Evaluate side-chains 96 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 265 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.189625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122490 restraints weight = 13701.966| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.23 r_work: 0.3059 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3020 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= 0.148 Angle : 0.569 9.017 14917 Z= 0.288 Chirality : 0.043 0.264 1737 Planarity : 0.004 0.064 1944 Dihedral : 4.724 49.889 1652 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 3.24 % Allowed : 16.01 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1468 helix: 1.77 (0.19), residues: 696 sheet: -1.04 (0.40), residues: 168 loop : -1.53 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 4 197 TYR 0.012 0.001 TYR 4 612 PHE 0.023 0.001 PHE 2 422 TRP 0.016 0.001 TRP 4 218 HIS 0.010 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00344 (10894) covalent geometry : angle 0.56344 (14874) SS BOND : bond 0.00266 ( 17) SS BOND : angle 1.15054 ( 34) hydrogen bonds : bond 0.04492 ( 553) hydrogen bonds : angle 4.28782 ( 1614) link_NAG-ASN : bond 0.00459 ( 3) link_NAG-ASN : angle 2.68475 ( 9) *********************** 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 118 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.363 Fit side-chains REVERT: 2 55 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7674 (mm-30) REVERT: 2 312 GLU cc_start: 0.8029 (tp30) cc_final: 0.7800 (mt-10) REVERT: 4 197 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8832 (ptt180) REVERT: 4 267 LYS cc_start: 0.7810 (tppt) cc_final: 0.7584 (ttmm) REVERT: 4 403 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7939 (tp30) REVERT: 4 817 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8544 (tp) REVERT: 4 837 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8265 (pp) outliers start: 32 outliers final: 13 residues processed: 110 average time/residue: 0.5246 time to fit residues: 63.2277 Evaluate side-chains 104 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 55 GLU Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 265 VAL 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 153 VAL Chi-restraints excluded: chain 4 residue 197 ARG 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 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 136 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.189925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.127089 restraints weight = 13590.680| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.10 r_work: 0.3087 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10914 Z= 0.146 Angle : 0.564 9.846 14917 Z= 0.283 Chirality : 0.042 0.253 1737 Planarity : 0.004 0.069 1944 Dihedral : 4.638 49.811 1652 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 2.94 % Allowed : 17.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1468 helix: 1.81 (0.19), residues: 700 sheet: -1.05 (0.40), residues: 168 loop : -1.50 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 61 TYR 0.012 0.001 TYR 4 612 PHE 0.022 0.001 PHE 2 422 TRP 0.014 0.001 TRP 4 218 HIS 0.009 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00339 (10894) covalent geometry : angle 0.55914 (14874) SS BOND : bond 0.00248 ( 17) SS BOND : angle 1.08006 ( 34) hydrogen bonds : bond 0.04378 ( 553) hydrogen bonds : angle 4.24223 ( 1614) link_NAG-ASN : bond 0.00449 ( 3) link_NAG-ASN : angle 2.48904 ( 9) *********************** 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 116 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.420 Fit side-chains REVERT: 2 55 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7852 (mm-30) REVERT: 2 312 GLU cc_start: 0.8205 (tp30) cc_final: 0.7877 (mt-10) REVERT: 4 197 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8867 (ptt180) REVERT: 4 267 LYS cc_start: 0.7996 (tppt) cc_final: 0.7794 (ttmm) REVERT: 4 403 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: 4 564 MET cc_start: 0.7920 (mtp) cc_final: 0.7293 (mpt) REVERT: 4 817 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8529 (tp) REVERT: 4 837 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8254 (pp) outliers start: 29 outliers final: 16 residues processed: 106 average time/residue: 0.5204 time to fit residues: 60.2539 Evaluate side-chains 105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 55 GLU Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 442 ARG 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 153 VAL Chi-restraints excluded: chain 4 residue 197 ARG Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 337 LYS 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 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 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4274 r_free = 0.4274 target = 0.190152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121018 restraints weight = 13632.338| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.39 r_work: 0.3052 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10914 Z= 0.133 Angle : 0.548 9.856 14917 Z= 0.277 Chirality : 0.042 0.241 1737 Planarity : 0.004 0.069 1944 Dihedral : 4.488 47.900 1652 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.44 % Rotamer: Outliers : 2.74 % Allowed : 17.43 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.22), residues: 1468 helix: 1.89 (0.19), residues: 702 sheet: -1.06 (0.40), residues: 168 loop : -1.47 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 61 TYR 0.011 0.001 TYR 4 612 PHE 0.022 0.001 PHE 2 422 TRP 0.013 0.001 TRP 4 218 HIS 0.009 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00305 (10894) covalent geometry : angle 0.54419 (14874) SS BOND : bond 0.00240 ( 17) SS BOND : angle 1.01458 ( 34) hydrogen bonds : bond 0.04180 ( 553) hydrogen bonds : angle 4.14927 ( 1614) link_NAG-ASN : bond 0.00438 ( 3) link_NAG-ASN : angle 2.27223 ( 9) *********************** 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 114 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.416 Fit side-chains REVERT: 2 55 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: 2 312 GLU cc_start: 0.8013 (tp30) cc_final: 0.7761 (mt-10) REVERT: 2 410 MET cc_start: 0.6683 (ttm) cc_final: 0.6290 (ttt) REVERT: 2 619 MET cc_start: 0.7044 (ptm) cc_final: 0.6748 (ptp) REVERT: 4 197 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8908 (ptt180) REVERT: 4 403 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7933 (tp30) REVERT: 4 564 MET cc_start: 0.7930 (mtp) cc_final: 0.7288 (mpt) REVERT: 4 837 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8265 (pp) outliers start: 27 outliers final: 16 residues processed: 106 average time/residue: 0.5070 time to fit residues: 59.1122 Evaluate side-chains 105 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 55 GLU Chi-restraints excluded: chain 2 residue 104 ASP Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 442 ARG 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 153 VAL Chi-restraints excluded: chain 4 residue 197 ARG 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 44 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.189598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119701 restraints weight = 13599.026| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.12 r_work: 0.3067 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10914 Z= 0.155 Angle : 0.575 10.596 14917 Z= 0.292 Chirality : 0.043 0.234 1737 Planarity : 0.004 0.073 1944 Dihedral : 4.581 49.619 1652 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 2.63 % Allowed : 17.73 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.22), residues: 1468 helix: 1.88 (0.19), residues: 702 sheet: -1.15 (0.40), residues: 170 loop : -1.47 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 107 TYR 0.011 0.001 TYR 4 179 PHE 0.022 0.001 PHE 2 422 TRP 0.013 0.001 TRP 4 218 HIS 0.009 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00366 (10894) covalent geometry : angle 0.57135 (14874) SS BOND : bond 0.00248 ( 17) SS BOND : angle 1.03442 ( 34) hydrogen bonds : bond 0.04372 ( 553) hydrogen bonds : angle 4.17508 ( 1614) link_NAG-ASN : bond 0.00409 ( 3) link_NAG-ASN : angle 2.22679 ( 9) *********************** 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 109 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.486 Fit side-chains REVERT: 2 55 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: 2 312 GLU cc_start: 0.8355 (tp30) cc_final: 0.8005 (mt-10) REVERT: 2 619 MET cc_start: 0.6970 (ptm) cc_final: 0.6682 (ptp) REVERT: 4 197 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8862 (ptt180) REVERT: 4 267 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7657 (tppt) REVERT: 4 403 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: 4 564 MET cc_start: 0.7985 (mtp) cc_final: 0.7312 (mpt) REVERT: 4 817 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8510 (tp) REVERT: 4 837 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8254 (pp) outliers start: 26 outliers final: 15 residues processed: 101 average time/residue: 0.5736 time to fit residues: 63.2215 Evaluate side-chains 102 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 55 GLU Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE 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 442 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 153 VAL Chi-restraints excluded: chain 4 residue 197 ARG 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 Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.186076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115586 restraints weight = 13426.393| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.20 r_work: 0.2993 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 10914 Z= 0.361 Angle : 0.737 12.036 14917 Z= 0.380 Chirality : 0.051 0.302 1737 Planarity : 0.006 0.085 1944 Dihedral : 5.386 61.760 1652 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 2.74 % Allowed : 17.43 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.22), residues: 1468 helix: 1.67 (0.19), residues: 694 sheet: -1.28 (0.40), residues: 169 loop : -1.76 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 4 170 TYR 0.025 0.003 TYR 4 179 PHE 0.024 0.003 PHE 2 422 TRP 0.026 0.003 TRP 4 314 HIS 0.009 0.002 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00877 (10894) covalent geometry : angle 0.73224 (14874) SS BOND : bond 0.00431 ( 17) SS BOND : angle 1.33263 ( 34) hydrogen bonds : bond 0.05713 ( 553) hydrogen bonds : angle 4.52316 ( 1614) link_NAG-ASN : bond 0.00475 ( 3) link_NAG-ASN : angle 2.91917 ( 9) ********************** 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 111 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.457 Fit side-chains REVERT: 2 55 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7990 (mm-30) REVERT: 2 65 MET cc_start: 0.9263 (ttt) cc_final: 0.9052 (ttt) REVERT: 2 222 GLU cc_start: 0.8080 (tt0) cc_final: 0.7815 (tt0) REVERT: 2 312 GLU cc_start: 0.8420 (tp30) cc_final: 0.8124 (mt-10) REVERT: 4 197 ARG cc_start: 0.9334 (OUTLIER) cc_final: 0.8961 (ptt180) REVERT: 4 403 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: 4 564 MET cc_start: 0.8004 (mtp) cc_final: 0.7774 (mtp) REVERT: 4 837 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8288 (pp) outliers start: 27 outliers final: 17 residues processed: 104 average time/residue: 0.5394 time to fit residues: 61.3931 Evaluate side-chains 104 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 55 GLU Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE 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 4 residue 108 THR Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 197 ARG Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 337 LYS Chi-restraints excluded: chain 4 residue 389 THR 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 804 ILE Chi-restraints excluded: chain 4 residue 837 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 92 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.189106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121397 restraints weight = 13664.803| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.35 r_work: 0.3069 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3459 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= 0.143 Angle : 0.583 10.549 14917 Z= 0.296 Chirality : 0.043 0.224 1737 Planarity : 0.004 0.080 1944 Dihedral : 4.839 54.388 1652 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Rotamer: Outliers : 2.13 % Allowed : 18.24 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.22), residues: 1468 helix: 1.83 (0.19), residues: 700 sheet: -1.17 (0.40), residues: 168 loop : -1.60 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 4 170 TYR 0.015 0.001 TYR 4 220 PHE 0.023 0.001 PHE 2 422 TRP 0.015 0.001 TRP 4 218 HIS 0.010 0.001 HIS 4 507 Details of bonding type rmsd covalent geometry : bond 0.00331 (10894) covalent geometry : angle 0.57757 (14874) SS BOND : bond 0.00293 ( 17) SS BOND : angle 1.26159 ( 34) hydrogen bonds : bond 0.04293 ( 553) hydrogen bonds : angle 4.23203 ( 1614) link_NAG-ASN : bond 0.00442 ( 3) link_NAG-ASN : angle 2.34899 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.17 seconds wall clock time: 78 minutes 27.15 seconds (4707.15 seconds total)