Starting phenix.real_space_refine on Fri Jan 19 07:14:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd4_36175/01_2024/8jd4_36175_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd4_36175/01_2024/8jd4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd4_36175/01_2024/8jd4_36175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd4_36175/01_2024/8jd4_36175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd4_36175/01_2024/8jd4_36175_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd4_36175/01_2024/8jd4_36175_neut.pdb" } 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 Residue "2 PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 397": "OD1" <-> "OD2" Residue "4 PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 2003": "OE1" <-> "OE2" Residue "4 GLU 1101": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 4 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 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: 6.40, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 4.48 Conformation dependent library (CDL) restraints added in 2.3 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: 1.42 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: 3.89 Time building geometry restraints manager: 4.81 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: 99.73 - 106.63: 334 106.63 - 113.52: 5965 113.52 - 120.42: 3992 120.42 - 127.31: 4460 127.31 - 134.21: 123 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 2.520 nonbonded pdb=" NE2 HIS 4 424 " pdb=" O GLY 4 433 " model vdw 2.310 2.520 nonbonded pdb=" NH1 ARG 2 452 " pdb=" O TYR 2 453 " model vdw 2.314 2.520 nonbonded pdb=" O ILE 2 324 " pdb=" NE2 GLN 2 374 " model vdw 2.314 2.520 nonbonded pdb=" NH2 ARG 2 264 " pdb=" O SER 2 288 " model vdw 2.331 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.700 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 33.930 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.050 ------------------------------------------------------------------------------- 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 10894 Z= 0.202 Angle : 0.526 6.700 14874 Z= 0.296 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.295 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: 1.1801 time to fit residues: 170.2572 Evaluate side-chains 99 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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: 0.4980 chunk 62 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10894 Z= 0.214 Angle : 0.558 8.750 14874 Z= 0.288 Chirality : 0.042 0.336 1737 Planarity : 0.004 0.045 1944 Dihedral : 7.210 74.968 1655 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.23 % Allowed : 8.51 % Favored : 89.26 % 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: 0.26 (0.22), residues: 1468 helix: 1.63 (0.19), residues: 700 sheet: -0.60 (0.41), residues: 164 loop : -1.38 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 4 218 HIS 0.002 0.001 HIS 4 498 PHE 0.027 0.001 PHE 2 422 TYR 0.014 0.001 TYR 4 548 ARG 0.004 0.000 ARG 4 78 *********************** 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 126 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.197 Fit side-chains REVERT: 2 411 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7616 (mpt90) REVERT: 4 44 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6653 (mtt180) REVERT: 4 267 LYS cc_start: 0.7931 (tmtm) cc_final: 0.7595 (ttmm) REVERT: 4 564 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7413 (mpp) outliers start: 22 outliers final: 5 residues processed: 112 average time/residue: 1.0645 time to fit residues: 130.8146 Evaluate side-chains 100 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 564 MET Chi-restraints excluded: chain 4 residue 821 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.4980 chunk 41 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 0.0020 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10894 Z= 0.190 Angle : 0.535 8.407 14874 Z= 0.270 Chirality : 0.042 0.321 1737 Planarity : 0.004 0.040 1944 Dihedral : 4.911 51.619 1652 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.13 % Allowed : 11.35 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.22), residues: 1468 helix: 1.82 (0.19), residues: 694 sheet: -0.70 (0.41), residues: 166 loop : -1.35 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 4 218 HIS 0.008 0.001 HIS 4 507 PHE 0.025 0.001 PHE 2 422 TYR 0.012 0.001 TYR 4 612 ARG 0.003 0.000 ARG 2 452 *********************** 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 120 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.284 Fit side-chains REVERT: 2 206 TYR cc_start: 0.7206 (t80) cc_final: 0.6824 (t80) REVERT: 4 564 MET cc_start: 0.7820 (mmm) cc_final: 0.7241 (mpt) outliers start: 21 outliers final: 7 residues processed: 113 average time/residue: 1.0561 time to fit residues: 131.4732 Evaluate side-chains 96 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 290 THR Chi-restraints excluded: chain 2 residue 424 LEU Chi-restraints excluded: chain 2 residue 509 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.0670 chunk 101 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 128 optimal weight: 30.0000 chunk 38 optimal weight: 0.0670 overall best weight: 0.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 414 ASN ** 4 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 176 GLN 4 359 ASN 4 402 GLN 4 507 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10894 Z= 0.130 Angle : 0.493 7.974 14874 Z= 0.246 Chirality : 0.040 0.294 1737 Planarity : 0.003 0.037 1944 Dihedral : 4.307 45.959 1652 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.13 % Allowed : 13.17 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1468 helix: 1.95 (0.20), residues: 700 sheet: -0.77 (0.39), residues: 176 loop : -1.32 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 218 HIS 0.010 0.001 HIS 4 507 PHE 0.020 0.001 PHE 2 422 TYR 0.012 0.001 TYR 4 612 ARG 0.002 0.000 ARG 2 452 *********************** 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 119 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 1.287 Fit side-chains REVERT: 2 206 TYR cc_start: 0.7300 (t80) cc_final: 0.6955 (t80) REVERT: 4 82 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8171 (ttt) REVERT: 4 564 MET cc_start: 0.7806 (mmm) cc_final: 0.7309 (mpt) REVERT: 4 837 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8218 (pp) outliers start: 21 outliers final: 6 residues processed: 110 average time/residue: 0.8395 time to fit residues: 104.2028 Evaluate side-chains 102 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 residue 82 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 0.0270 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 122 optimal weight: 0.0770 chunk 98 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 overall best weight: 1.0318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 4 176 GLN 4 359 ASN 4 507 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10894 Z= 0.288 Angle : 0.582 8.948 14874 Z= 0.294 Chirality : 0.043 0.281 1737 Planarity : 0.004 0.037 1944 Dihedral : 4.759 53.556 1652 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 3.14 % Allowed : 14.18 % Favored : 82.67 % 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: 0.50 (0.22), residues: 1468 helix: 1.99 (0.20), residues: 690 sheet: -0.78 (0.41), residues: 166 loop : -1.33 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 314 HIS 0.010 0.001 HIS 4 507 PHE 0.025 0.002 PHE 2 422 TYR 0.013 0.002 TYR 2 165 ARG 0.005 0.001 ARG 2 61 *********************** 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 125 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.124 Fit side-chains REVERT: 4 219 ASN cc_start: 0.7534 (m-40) cc_final: 0.7091 (m-40) REVERT: 4 267 LYS cc_start: 0.7965 (ttmm) cc_final: 0.7556 (tppt) REVERT: 4 564 MET cc_start: 0.7751 (mmm) cc_final: 0.7301 (mpt) REVERT: 4 837 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8264 (pp) outliers start: 31 outliers final: 11 residues processed: 113 average time/residue: 0.9780 time to fit residues: 122.1051 Evaluate side-chains 98 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 463 VAL Chi-restraints excluded: chain 4 residue 515 LEU Chi-restraints excluded: chain 4 residue 804 ILE Chi-restraints excluded: chain 4 residue 808 THR Chi-restraints excluded: chain 4 residue 820 THR 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 48 optimal weight: 8.9990 chunk 128 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10894 Z= 0.210 Angle : 0.542 9.133 14874 Z= 0.272 Chirality : 0.042 0.261 1737 Planarity : 0.004 0.033 1944 Dihedral : 4.561 53.324 1652 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer: Outliers : 2.63 % Allowed : 15.60 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1468 helix: 1.94 (0.20), residues: 705 sheet: -0.78 (0.41), residues: 166 loop : -1.35 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 4 218 HIS 0.002 0.001 HIS 2 390 PHE 0.025 0.001 PHE 2 422 TYR 0.012 0.001 TYR 4 612 ARG 0.003 0.000 ARG 2 61 *********************** 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 113 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 1.107 Fit side-chains REVERT: 4 219 ASN cc_start: 0.7539 (m-40) cc_final: 0.7136 (m-40) REVERT: 4 267 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7571 (tppt) REVERT: 4 564 MET cc_start: 0.7868 (mmm) cc_final: 0.7367 (mpt) REVERT: 4 837 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8259 (pp) outliers start: 26 outliers final: 15 residues processed: 103 average time/residue: 0.8772 time to fit residues: 101.1750 Evaluate side-chains 102 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 509 VAL Chi-restraints excluded: chain 2 residue 770 CYS 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 187 SER 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 808 THR 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 138 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 507 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 10894 Z= 0.503 Angle : 0.695 11.950 14874 Z= 0.355 Chirality : 0.048 0.240 1737 Planarity : 0.006 0.075 1944 Dihedral : 5.292 60.098 1652 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 3.24 % Allowed : 16.31 % 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: 0.24 (0.22), residues: 1468 helix: 1.77 (0.19), residues: 698 sheet: -0.80 (0.40), residues: 170 loop : -1.54 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP 4 314 HIS 0.011 0.001 HIS 4 507 PHE 0.029 0.002 PHE 2 422 TYR 0.022 0.002 TYR 4 179 ARG 0.009 0.001 ARG 4 197 *********************** 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 125 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 1.179 Fit side-chains REVERT: 4 219 ASN cc_start: 0.7754 (m-40) cc_final: 0.7483 (m-40) REVERT: 4 438 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.4416 (tpt) REVERT: 4 506 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7636 (mtm) REVERT: 4 564 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7463 (mtp) REVERT: 4 837 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8284 (pp) outliers start: 32 outliers final: 16 residues processed: 111 average time/residue: 1.0283 time to fit residues: 125.7221 Evaluate side-chains 103 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 227 GLU 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 119 SER Chi-restraints excluded: chain 4 residue 153 VAL Chi-restraints excluded: chain 4 residue 214 ARG Chi-restraints excluded: chain 4 residue 337 LYS Chi-restraints excluded: chain 4 residue 354 ASP Chi-restraints excluded: chain 4 residue 428 CYS Chi-restraints excluded: chain 4 residue 438 MET Chi-restraints excluded: chain 4 residue 463 VAL Chi-restraints excluded: chain 4 residue 506 MET Chi-restraints excluded: chain 4 residue 507 HIS Chi-restraints excluded: chain 4 residue 564 MET Chi-restraints excluded: chain 4 residue 804 ILE Chi-restraints excluded: chain 4 residue 808 THR 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 56 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 112 optimal weight: 0.0000 chunk 129 optimal weight: 0.0980 overall best weight: 0.1742 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10894 Z= 0.158 Angle : 0.541 13.904 14874 Z= 0.268 Chirality : 0.041 0.241 1737 Planarity : 0.004 0.061 1944 Dihedral : 4.585 51.760 1652 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 1.82 % Allowed : 17.73 % 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: 0.49 (0.22), residues: 1468 helix: 2.04 (0.20), residues: 701 sheet: -1.01 (0.38), residues: 178 loop : -1.42 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 4 218 HIS 0.017 0.001 HIS 4 507 PHE 0.021 0.001 PHE 2 422 TYR 0.016 0.001 TYR 4 220 ARG 0.003 0.000 ARG 4 214 *********************** 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 fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.731 Fit side-chains REVERT: 4 219 ASN cc_start: 0.7501 (m-40) cc_final: 0.7153 (m-40) REVERT: 4 267 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7544 (tppt) REVERT: 4 837 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8247 (pp) outliers start: 18 outliers final: 10 residues processed: 96 average time/residue: 0.9494 time to fit residues: 101.4898 Evaluate side-chains 91 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE 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 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 808 THR 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 136 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.110 10894 Z= 0.766 Angle : 0.827 13.089 14874 Z= 0.426 Chirality : 0.056 0.380 1737 Planarity : 0.007 0.117 1944 Dihedral : 5.673 62.262 1652 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 18.03 % Favored : 79.23 % 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: 1.60 (0.19), residues: 700 sheet: -1.12 (0.40), residues: 163 loop : -1.79 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP 4 314 HIS 0.013 0.002 HIS 4 507 PHE 0.029 0.003 PHE 2 422 TYR 0.029 0.003 TYR 4 179 ARG 0.012 0.001 ARG 4 197 *********************** 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 114 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 1.317 Fit side-chains REVERT: 2 222 GLU cc_start: 0.7205 (tt0) cc_final: 0.6994 (tt0) REVERT: 2 619 MET cc_start: 0.6673 (ptm) cc_final: 0.6410 (ptp) REVERT: 4 309 MET cc_start: 0.8673 (ttm) cc_final: 0.8469 (ttm) REVERT: 4 506 MET cc_start: 0.8033 (mtm) cc_final: 0.7600 (mtp) REVERT: 4 817 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8520 (tp) REVERT: 4 837 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8298 (pp) outliers start: 27 outliers final: 13 residues processed: 103 average time/residue: 0.9413 time to fit residues: 107.9587 Evaluate side-chains 99 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 227 GLU 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 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 804 ILE Chi-restraints excluded: chain 4 residue 808 THR Chi-restraints excluded: chain 4 residue 817 ILE Chi-restraints excluded: chain 4 residue 821 THR 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 85 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 125 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 507 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10894 Z= 0.222 Angle : 0.581 13.025 14874 Z= 0.291 Chirality : 0.042 0.218 1737 Planarity : 0.005 0.085 1944 Dihedral : 5.019 55.395 1652 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.64 % Rotamer: Outliers : 1.32 % Allowed : 19.15 % Favored : 79.53 % 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: 0.28 (0.22), residues: 1468 helix: 1.89 (0.20), residues: 704 sheet: -1.12 (0.39), residues: 170 loop : -1.56 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 218 HIS 0.011 0.001 HIS 4 507 PHE 0.026 0.001 PHE 2 422 TYR 0.018 0.001 TYR 4 220 ARG 0.003 0.000 ARG 4 78 ********************** 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 98 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.221 Fit side-chains REVERT: 2 619 MET cc_start: 0.6538 (ptm) cc_final: 0.6304 (ptp) REVERT: 4 837 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8267 (pp) outliers start: 13 outliers final: 10 residues processed: 94 average time/residue: 0.9973 time to fit residues: 104.5069 Evaluate side-chains 95 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 509 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 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 35 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.188616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115362 restraints weight = 13508.719| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.06 r_work: 0.3075 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10894 Z= 0.251 Angle : 0.594 12.849 14874 Z= 0.299 Chirality : 0.042 0.214 1737 Planarity : 0.005 0.082 1944 Dihedral : 4.916 53.989 1652 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 1.93 % Allowed : 18.64 % Favored : 79.43 % 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 (0.20), residues: 705 sheet: -1.00 (0.40), residues: 168 loop : -1.57 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 218 HIS 0.012 0.001 HIS 4 507 PHE 0.019 0.001 PHE 2 422 TYR 0.013 0.002 TYR 4 220 ARG 0.003 0.000 ARG 2 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.36 seconds wall clock time: 61 minutes 26.90 seconds (3686.90 seconds total)