Starting phenix.real_space_refine on Fri Jul 3 00:29:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcw_36167/07_2026/8jcw_36167.map" } resolution = 3.0 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= 0.070 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 64 5.16 5 C 6806 2.51 5 N 1869 2.21 5 O 2021 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10760 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5266 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 37, 'TRANS': 724} Chain breaks: 2 Unresolved non-hydrogen bonds: 696 Unresolved non-hydrogen angles: 890 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 21, 'ASP:plan': 6, 'GLN:plan1': 6, 'ASN:plan1': 6, 'HIS:plan': 4, 'PHE:plan': 14, 'TYR:plan': 7, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 397 Chain: "3" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5358 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 936 Unresolved non-hydrogen dihedrals: 608 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 12, 'ARG:plan': 14, 'GLN:plan1': 5, 'HIS:plan': 4, 'ASP:plan': 11, 'TYR:plan': 9, 'TRP:plan': 3, 'PHE:plan': 12} Unresolved non-hydrogen planarities: 385 Chain: "2" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'CLR': 1, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'CLR': 1, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.45, per 1000 atoms: 0.23 Number of scatterers: 10760 At special positions: 0 Unit cell: (88.893, 124.236, 184.212, 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 64 16.00 O 2021 8.00 N 1869 7.00 C 6806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 21101 " - " ASN 2 203 " " NAG 31001 " - " ASN 3 209 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 374.1 milliseconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 47.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain '2' and resid 44 through 48 removed outlier: 4.052A pdb=" N ALA 2 47 " --> pdb=" O GLY 2 44 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU 2 48 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 44 through 48' Processing helix chain '2' and resid 58 through 74 removed outlier: 3.639A pdb=" N LEU 2 62 " --> pdb=" O GLY 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 94 through 107 removed outlier: 3.697A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 157 removed outlier: 4.321A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 169 through 173 removed outlier: 3.619A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 169 through 173' Processing helix chain '2' and resid 189 through 202 Processing helix chain '2' and resid 214 through 230 removed outlier: 6.384A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 removed outlier: 3.928A pdb=" N PHE 2 250 " --> pdb=" O SER 2 246 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 285 removed outlier: 3.684A pdb=" N GLU 2 277 " --> pdb=" O GLU 2 273 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) Processing helix chain '2' and resid 324 through 333 removed outlier: 3.534A pdb=" N SER 2 333 " --> pdb=" O SER 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 344 through 354 Processing helix chain '2' and resid 377 through 400 Processing helix chain '2' and resid 414 through 422 Processing helix chain '2' and resid 569 through 592 Processing helix chain '2' and resid 593 through 595 No H-bonds generated for 'chain '2' and resid 593 through 595' Processing helix chain '2' and resid 602 through 624 Processing helix chain '2' and resid 630 through 659 removed outlier: 4.389A pdb=" N LYS 2 653 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR 2 654 " --> pdb=" O LEU 2 650 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 701 removed outlier: 3.620A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) Processing helix chain '2' and resid 724 through 748 removed outlier: 3.776A pdb=" N MET 2 728 " --> pdb=" O ARG 2 724 " (cutoff:3.500A) Processing helix chain '2' and resid 755 through 784 removed outlier: 4.871A pdb=" N PHE 2 761 " --> pdb=" O ASN 2 757 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR 2 767 " --> pdb=" O GLY 2 763 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR 2 768 " --> pdb=" O PHE 2 764 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix removed outlier: 3.757A pdb=" N TYR 2 781 " --> pdb=" O LEU 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 818 removed outlier: 3.629A pdb=" N THR 2 791 " --> pdb=" O TYR 2 787 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 65 through 81 Processing helix chain '3' and resid 101 through 109 Processing helix chain '3' and resid 109 through 114 removed outlier: 3.656A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 115 through 117 No H-bonds generated for 'chain '3' and resid 115 through 117' Processing helix chain '3' and resid 150 through 162 Processing helix chain '3' and resid 175 through 180 Processing helix chain '3' and resid 194 through 208 removed outlier: 3.815A pdb=" N ALA 3 198 " --> pdb=" O ASP 3 194 " (cutoff:3.500A) Processing helix chain '3' and resid 221 through 237 Processing helix chain '3' and resid 254 through 265 Processing helix chain '3' and resid 279 through 291 Processing helix chain '3' and resid 330 through 339 removed outlier: 3.539A pdb=" N ASP 3 334 " --> pdb=" O VAL 3 330 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 389 through 412 removed outlier: 3.806A pdb=" N VAL 3 393 " --> pdb=" O LYS 3 389 " (cutoff:3.500A) Processing helix chain '3' and resid 419 through 423 Processing helix chain '3' and resid 426 through 435 Processing helix chain '3' and resid 578 through 601 Processing helix chain '3' and resid 611 through 632 removed outlier: 3.773A pdb=" N PHE 3 632 " --> pdb=" O MET 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 637 through 664 removed outlier: 3.747A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 682 through 707 Processing helix chain '3' and resid 717 through 721 removed outlier: 4.103A pdb=" N GLU 3 721 " --> pdb=" O THR 3 718 " (cutoff:3.500A) Processing helix chain '3' and resid 731 through 733 No H-bonds generated for 'chain '3' and resid 731 through 733' Processing helix chain '3' and resid 734 through 756 removed outlier: 3.689A pdb=" N ASP 3 744 " --> pdb=" O SER 3 740 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL 3 745 " --> pdb=" O LEU 3 741 " (cutoff:3.500A) Processing helix chain '3' and resid 764 through 792 removed outlier: 4.193A pdb=" N ALA 3 768 " --> pdb=" O ASN 3 764 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 4.029A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 796 through 826 removed outlier: 3.885A pdb=" N THR 3 800 " --> pdb=" O TYR 3 796 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS 3 817 " --> pdb=" O VAL 3 813 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU 3 818 " --> pdb=" O VAL 3 814 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE 3 819 " --> pdb=" O LEU 3 815 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 84 through 90 removed outlier: 6.578A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 234 through 240 removed outlier: 7.938A pdb=" N VAL 2 207 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N SER 2 238 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR 2 209 " --> pdb=" O SER 2 238 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS 2 240 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA 2 211 " --> pdb=" O LYS 2 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE 2 269 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL 2 210 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA 2 266 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG 2 467 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR 2 473 " --> pdb=" O THR 2 479 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 428 through 429 removed outlier: 3.693A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 508 through 511 Processing sheet with id=AA5, first strand: chain '2' and resid 529 through 530 Processing sheet with id=AA6, first strand: chain '3' and resid 33 through 34 removed outlier: 6.394A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 48 through 50 removed outlier: 5.370A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 240 through 246 removed outlier: 7.779A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE 3 275 " --> pdb=" O SER 3 214 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL 3 216 " --> pdb=" O PHE 3 275 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 440 through 441 removed outlier: 3.687A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 518 through 521 Processing sheet with id=AB2, first strand: chain '3' and resid 538 through 539 Processing sheet with id=AB3, first strand: chain '3' and resid 554 through 555 548 hydrogen bonds defined for protein. 1602 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: 1.80 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: 3473 1.34 - 1.46: 1630 1.46 - 1.58: 5806 1.58 - 1.70: 1 1.70 - 1.82: 82 Bond restraints: 10992 Sorted by residual: bond pdb=" CAT Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.364 1.461 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" CAT Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.364 1.457 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAS Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" CAS Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C ASN 3 445 " pdb=" N PRO 3 446 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.77e+00 ... (remaining 10987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 14854 2.26 - 4.52: 156 4.52 - 6.78: 28 6.78 - 9.04: 12 9.04 - 11.31: 4 Bond angle restraints: 15054 Sorted by residual: angle pdb=" CA PRO 2 524 " pdb=" N PRO 2 524 " pdb=" CD PRO 2 524 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" CB ARG 3 183 " pdb=" CG ARG 3 183 " pdb=" CD ARG 3 183 " ideal model delta sigma weight residual 111.30 100.30 11.00 2.30e+00 1.89e-01 2.29e+01 angle pdb=" N GLU 2 225 " pdb=" CA GLU 2 225 " pdb=" CB GLU 2 225 " ideal model delta sigma weight residual 110.12 116.36 -6.24 1.47e+00 4.63e-01 1.80e+01 angle pdb=" C ARG 3 183 " pdb=" CA ARG 3 183 " pdb=" CB ARG 3 183 " ideal model delta sigma weight residual 109.15 116.45 -7.30 1.78e+00 3.16e-01 1.68e+01 angle pdb=" CAX Z99 21102 " pdb=" CAZ Z99 21102 " pdb=" CAY Z99 21102 " ideal model delta sigma weight residual 120.67 109.36 11.31 3.00e+00 1.11e-01 1.42e+01 ... (remaining 15049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 6043 17.57 - 35.14: 363 35.14 - 52.71: 65 52.71 - 70.28: 15 70.28 - 87.84: 9 Dihedral angle restraints: 6495 sinusoidal: 2064 harmonic: 4431 Sorted by residual: dihedral pdb=" CB CYS 2 632 " pdb=" SG CYS 2 632 " pdb=" SG CYS 2 721 " pdb=" CB CYS 2 721 " ideal model delta sinusoidal sigma weight residual -86.00 1.84 -87.84 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS 3 412 " pdb=" SG CYS 3 412 " pdb=" SG CYS 3 419 " pdb=" CB CYS 3 419 " ideal model delta sinusoidal sigma weight residual 93.00 170.52 -77.52 1 1.00e+01 1.00e-02 7.53e+01 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 93.00 29.36 63.64 1 1.00e+01 1.00e-02 5.34e+01 ... (remaining 6492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.973: 1752 0.973 - 1.947: 0 1.947 - 2.920: 0 2.920 - 3.893: 0 3.893 - 4.866: 2 Chirality restraints: 1754 Sorted by residual: chirality pdb=" CAW Z99 21102 " pdb=" CAN Z99 21102 " pdb=" CAU Z99 21102 " pdb=" CAV Z99 21102 " both_signs ideal model delta sigma weight residual False 2.61 -2.26 4.87 2.00e-01 2.50e+01 5.92e+02 chirality pdb=" CAW Z99 31002 " pdb=" CAN Z99 31002 " pdb=" CAU Z99 31002 " pdb=" CAV Z99 31002 " both_signs ideal model delta sigma weight residual False 2.61 -2.15 4.76 2.00e-01 2.50e+01 5.67e+02 chirality pdb=" CAY Z99 31002 " pdb=" CAN Z99 31002 " pdb=" CAR Z99 31002 " pdb=" CAZ Z99 31002 " both_signs ideal model delta sigma weight residual False -2.97 -2.58 -0.39 2.00e-01 2.50e+01 3.82e+00 ... (remaining 1751 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 2 523 " -0.079 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO 2 524 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO 2 524 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO 2 524 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP 3 706 " 0.014 2.00e-02 2.50e+03 1.14e-02 3.27e+00 pdb=" CG TRP 3 706 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP 3 706 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP 3 706 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP 3 706 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP 3 706 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP 3 706 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP 3 706 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP 3 706 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP 3 706 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR 3 431 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C TYR 3 431 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR 3 431 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS 3 432 " 0.010 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1404 2.75 - 3.29: 10446 3.29 - 3.83: 18073 3.83 - 4.36: 19713 4.36 - 4.90: 34809 Nonbonded interactions: 84445 Sorted by model distance: nonbonded pdb=" OG SER 2 262 " pdb=" O SER 2 498 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN 3 232 " pdb=" NH2 ARG 3 235 " model vdw 2.243 3.120 nonbonded pdb=" O TYR 3 212 " pdb=" OG SER 3 507 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU 3 224 " pdb=" NZ LYS 3 246 " model vdw 2.295 3.120 nonbonded pdb=" O SER 2 169 " pdb=" NH1 ARG 2 183 " model vdw 2.312 3.120 ... (remaining 84440 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=0.50 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: 3.020 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 0.109 11012 Z= 0.151 Angle : 0.611 11.306 15096 Z= 0.296 Chirality : 0.168 4.866 1754 Planarity : 0.004 0.116 1972 Dihedral : 11.924 81.906 3575 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % 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 are not related in a simple way. whole: 0.47 (0.22), residues: 1515 helix: 2.39 (0.20), residues: 681 sheet: -0.86 (0.44), residues: 149 loop : -1.68 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 183 TYR 0.008 0.001 TYR 3 563 PHE 0.012 0.001 PHE 3 544 TRP 0.032 0.001 TRP 3 706 HIS 0.002 0.000 HIS 2 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (10992) covalent geometry : angle 0.61037 / 0.30 (15054) SS BOND : bond 0.00238 / 0.13 ( 18) SS BOND : angle 0.78933 / 0.52 ( 36) hydrogen bonds : bond 0.15789 / 10.37 ( 548) hydrogen bonds : angle 5.00028 / 3.71 ( 1602) link_NAG-ASN : bond 0.00205 / 0.10 ( 2) link_NAG-ASN : angle 1.00006 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: 2 259 GLN cc_start: 0.8104 (pt0) cc_final: 0.7724 (pp30) REVERT: 2 518 CYS cc_start: 0.1891 (p) cc_final: 0.1307 (p) outliers start: 2 outliers final: 0 residues processed: 136 average time/residue: 0.4326 time to fit residues: 64.2603 Evaluate side-chains 99 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 94 HIS 3 232 GLN 3 251 ASN 3 341 ASN 3 470 ASN 3 472 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.207896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128032 restraints weight = 12781.853| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.81 r_work: 0.3216 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11012 Z= 0.208 Angle : 0.618 11.542 15096 Z= 0.311 Chirality : 0.044 0.257 1754 Planarity : 0.004 0.056 1972 Dihedral : 4.639 59.146 1649 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.39 % Allowed : 9.36 % Favored : 88.25 % 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 are not related in a simple way. whole: 0.36 (0.22), residues: 1515 helix: 2.35 (0.20), residues: 676 sheet: -0.81 (0.42), residues: 138 loop : -1.79 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 253 TYR 0.017 0.002 TYR 3 171 PHE 0.018 0.002 PHE 2 327 TRP 0.022 0.001 TRP 3 706 HIS 0.003 0.001 HIS 2 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (10992) covalent geometry : angle 0.61689 / 0.31 (15054) SS BOND : bond 0.00295 / 0.18 ( 18) SS BOND : angle 0.84276 / 0.52 ( 36) hydrogen bonds : bond 0.03999 / 2.79 ( 548) hydrogen bonds : angle 4.01982 / 2.93 ( 1602) link_NAG-ASN : bond 0.00324 / 0.15 ( 2) link_NAG-ASN : angle 0.88915 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: 2 229 ARG cc_start: 0.7475 (mtm110) cc_final: 0.7234 (mmt180) REVERT: 2 259 GLN cc_start: 0.8045 (pt0) cc_final: 0.7551 (pp30) REVERT: 2 356 SER cc_start: 0.8342 (m) cc_final: 0.7623 (p) REVERT: 3 59 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7996 (ptm160) REVERT: 3 183 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7345 (mtp85) REVERT: 3 328 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: 3 803 MET cc_start: 0.6527 (mmm) cc_final: 0.6196 (mmm) outliers start: 22 outliers final: 10 residues processed: 121 average time/residue: 0.3991 time to fit residues: 53.0243 Evaluate side-chains 108 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 177 LYS Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 328 GLN Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 497 ILE Chi-restraints excluded: chain 3 residue 518 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 61 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 141 optimal weight: 0.0270 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 168 GLN 3 232 GLN 3 251 ASN 3 344 ASN 3 470 ASN 3 508 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.207950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128763 restraints weight = 12747.146| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.83 r_work: 0.3223 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11012 Z= 0.143 Angle : 0.544 10.033 15096 Z= 0.273 Chirality : 0.042 0.184 1754 Planarity : 0.004 0.037 1972 Dihedral : 4.518 54.485 1649 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.72 % Allowed : 12.19 % Favored : 85.09 % 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 are not related in a simple way. whole: 0.43 (0.22), residues: 1515 helix: 2.45 (0.20), residues: 679 sheet: -0.99 (0.42), residues: 139 loop : -1.78 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 335 TYR 0.011 0.001 TYR 3 222 PHE 0.012 0.001 PHE 3 195 TRP 0.019 0.001 TRP 3 706 HIS 0.002 0.001 HIS 3 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10992) covalent geometry : angle 0.54353 / 0.27 (15054) SS BOND : bond 0.00220 / 0.13 ( 18) SS BOND : angle 0.76610 / 0.44 ( 36) hydrogen bonds : bond 0.03601 / 2.44 ( 548) hydrogen bonds : angle 3.78913 / 2.76 ( 1602) link_NAG-ASN : bond 0.00090 / 0.04 ( 2) link_NAG-ASN : angle 0.94463 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: 2 259 GLN cc_start: 0.8016 (pt0) cc_final: 0.7546 (pp30) REVERT: 2 356 SER cc_start: 0.8354 (m) cc_final: 0.7577 (p) REVERT: 2 469 GLN cc_start: 0.8017 (mt0) cc_final: 0.7775 (tt0) REVERT: 3 59 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7885 (ptm160) REVERT: 3 72 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7293 (ttt) REVERT: 3 803 MET cc_start: 0.6529 (mmm) cc_final: 0.6189 (mmm) outliers start: 25 outliers final: 13 residues processed: 109 average time/residue: 0.4022 time to fit residues: 48.4978 Evaluate side-chains 106 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 85 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 61 optimal weight: 40.0000 chunk 63 optimal weight: 10.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 232 GLN 3 251 ASN 3 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.206797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125040 restraints weight = 12790.469| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.37 r_work: 0.3211 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11012 Z= 0.147 Angle : 0.541 10.265 15096 Z= 0.272 Chirality : 0.042 0.199 1754 Planarity : 0.004 0.046 1972 Dihedral : 4.496 53.216 1649 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.94 % Allowed : 13.28 % Favored : 83.79 % 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 are not related in a simple way. whole: 0.43 (0.22), residues: 1515 helix: 2.42 (0.20), residues: 685 sheet: -0.82 (0.43), residues: 137 loop : -1.81 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 229 TYR 0.010 0.001 TYR 3 171 PHE 0.014 0.001 PHE 3 195 TRP 0.017 0.001 TRP 3 706 HIS 0.002 0.001 HIS 2 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (10992) covalent geometry : angle 0.54047 / 0.27 (15054) SS BOND : bond 0.00202 / 0.12 ( 18) SS BOND : angle 0.65876 / 0.39 ( 36) hydrogen bonds : bond 0.03415 / 2.33 ( 548) hydrogen bonds : angle 3.71234 / 2.70 ( 1602) link_NAG-ASN : bond 0.00103 / 0.05 ( 2) link_NAG-ASN : angle 0.90830 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: 2 259 GLN cc_start: 0.8026 (pt0) cc_final: 0.7546 (pp30) REVERT: 2 356 SER cc_start: 0.8343 (m) cc_final: 0.7499 (p) REVERT: 3 59 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7974 (ptm160) REVERT: 3 183 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7294 (mtp85) REVERT: 3 335 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8159 (ttp-110) REVERT: 3 520 ASN cc_start: 0.6753 (p0) cc_final: 0.6529 (p0) REVERT: 3 803 MET cc_start: 0.6623 (mmm) cc_final: 0.6291 (mmm) outliers start: 27 outliers final: 14 residues processed: 115 average time/residue: 0.3905 time to fit residues: 50.0964 Evaluate side-chains 108 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 232 GLN 3 251 ASN 3 344 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.208059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132635 restraints weight = 12724.471| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.59 r_work: 0.3243 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11012 Z= 0.111 Angle : 0.508 8.917 15096 Z= 0.256 Chirality : 0.041 0.197 1754 Planarity : 0.003 0.041 1972 Dihedral : 4.301 52.637 1649 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.26 % Allowed : 14.04 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1515 helix: 2.49 (0.20), residues: 686 sheet: -0.77 (0.43), residues: 136 loop : -1.77 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 229 TYR 0.008 0.001 TYR 2 473 PHE 0.011 0.001 PHE 3 195 TRP 0.016 0.001 TRP 3 706 HIS 0.001 0.000 HIS 2 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10992) covalent geometry : angle 0.50745 / 0.26 (15054) SS BOND : bond 0.00179 / 0.10 ( 18) SS BOND : angle 0.60428 / 0.35 ( 36) hydrogen bonds : bond 0.03110 / 2.13 ( 548) hydrogen bonds : angle 3.61965 / 2.63 ( 1602) link_NAG-ASN : bond 0.00089 / 0.04 ( 2) link_NAG-ASN : angle 0.93999 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 65 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7590 (ttt) REVERT: 2 227 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: 2 259 GLN cc_start: 0.8015 (pt0) cc_final: 0.7561 (pp30) REVERT: 2 356 SER cc_start: 0.8364 (m) cc_final: 0.7552 (p) REVERT: 3 59 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7906 (ptm160) REVERT: 3 72 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7255 (ttt) REVERT: 3 183 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7304 (mtp85) REVERT: 3 520 ASN cc_start: 0.6765 (p0) cc_final: 0.6530 (p0) REVERT: 3 803 MET cc_start: 0.6596 (mmm) cc_final: 0.6237 (mmm) outliers start: 30 outliers final: 17 residues processed: 113 average time/residue: 0.3993 time to fit residues: 50.2942 Evaluate side-chains 110 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 86 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 2 414 ASN 3 232 GLN 3 251 ASN 3 341 ASN 3 473 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.206200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130084 restraints weight = 12673.537| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.88 r_work: 0.3169 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11012 Z= 0.157 Angle : 0.554 10.320 15096 Z= 0.278 Chirality : 0.042 0.196 1754 Planarity : 0.004 0.061 1972 Dihedral : 4.443 53.916 1649 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.48 % Allowed : 14.58 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1515 helix: 2.45 (0.20), residues: 686 sheet: -0.89 (0.42), residues: 142 loop : -1.82 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 2 229 TYR 0.011 0.001 TYR 3 171 PHE 0.014 0.001 PHE 3 195 TRP 0.016 0.001 TRP 3 706 HIS 0.002 0.001 HIS 2 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (10992) covalent geometry : angle 0.55372 / 0.28 (15054) SS BOND : bond 0.00173 / 0.10 ( 18) SS BOND : angle 0.65858 / 0.38 ( 36) hydrogen bonds : bond 0.03393 / 2.31 ( 548) hydrogen bonds : angle 3.64869 / 2.65 ( 1602) link_NAG-ASN : bond 0.00059 / 0.03 ( 2) link_NAG-ASN : angle 0.88255 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: 2 259 GLN cc_start: 0.7953 (pt0) cc_final: 0.7480 (pp30) REVERT: 2 356 SER cc_start: 0.8300 (m) cc_final: 0.7423 (p) REVERT: 3 59 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: 3 72 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7361 (ttt) REVERT: 3 183 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7326 (mtp85) REVERT: 3 363 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6357 (mm) REVERT: 3 520 ASN cc_start: 0.6776 (p0) cc_final: 0.6555 (p0) REVERT: 3 803 MET cc_start: 0.6648 (mmm) cc_final: 0.6281 (mmm) outliers start: 32 outliers final: 18 residues processed: 116 average time/residue: 0.4016 time to fit residues: 51.6483 Evaluate side-chains 113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 236 LEU Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 118 optimal weight: 0.4980 chunk 70 optimal weight: 0.0170 chunk 7 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 40 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 232 GLN 3 251 ASN 3 341 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.207870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132268 restraints weight = 12721.501| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.79 r_work: 0.3209 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11012 Z= 0.110 Angle : 0.522 9.886 15096 Z= 0.262 Chirality : 0.041 0.203 1754 Planarity : 0.004 0.067 1972 Dihedral : 4.336 53.136 1649 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.16 % Allowed : 14.69 % Favored : 82.15 % 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 are not related in a simple way. whole: 0.52 (0.22), residues: 1515 helix: 2.51 (0.20), residues: 686 sheet: -0.82 (0.43), residues: 141 loop : -1.78 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 229 TYR 0.009 0.001 TYR 3 196 PHE 0.011 0.001 PHE 3 195 TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10992) covalent geometry : angle 0.52138 / 0.26 (15054) SS BOND : bond 0.00192 / 0.10 ( 18) SS BOND : angle 0.64178 / 0.37 ( 36) hydrogen bonds : bond 0.03054 / 2.10 ( 548) hydrogen bonds : angle 3.56877 / 2.59 ( 1602) link_NAG-ASN : bond 0.00087 / 0.04 ( 2) link_NAG-ASN : angle 0.91666 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 65 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7633 (ttt) REVERT: 2 227 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: 2 259 GLN cc_start: 0.7970 (pt0) cc_final: 0.7499 (pp30) REVERT: 2 356 SER cc_start: 0.8344 (m) cc_final: 0.7429 (p) REVERT: 3 59 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7880 (ptm160) REVERT: 3 183 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.7257 (mtp85) REVERT: 3 335 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.8024 (tmm160) REVERT: 3 363 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6387 (mm) REVERT: 3 803 MET cc_start: 0.6656 (mmm) cc_final: 0.6272 (mmm) outliers start: 29 outliers final: 17 residues processed: 112 average time/residue: 0.3919 time to fit residues: 49.2051 Evaluate side-chains 111 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 262 SER Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 135 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 168 GLN 3 232 GLN 3 251 ASN 3 341 ASN 3 473 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.202811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120521 restraints weight = 12742.396| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.70 r_work: 0.3100 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 11012 Z= 0.326 Angle : 0.709 13.636 15096 Z= 0.353 Chirality : 0.048 0.225 1754 Planarity : 0.005 0.079 1972 Dihedral : 5.128 56.957 1649 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.70 % Allowed : 14.15 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 0.12 (0.22), residues: 1515 helix: 2.20 (0.20), residues: 689 sheet: -1.10 (0.42), residues: 143 loop : -2.02 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 2 229 TYR 0.020 0.002 TYR 3 186 PHE 0.018 0.002 PHE 3 195 TRP 0.019 0.002 TRP 2 487 HIS 0.003 0.001 HIS 3 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.33 (10992) covalent geometry : angle 0.70838 / 0.35 (15054) SS BOND : bond 0.00214 / 0.14 ( 18) SS BOND : angle 0.95159 / 0.55 ( 36) hydrogen bonds : bond 0.04440 / 2.96 ( 548) hydrogen bonds : angle 3.95218 / 2.88 ( 1602) link_NAG-ASN : bond 0.00339 / 0.17 ( 2) link_NAG-ASN : angle 0.94224 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: 2 259 GLN cc_start: 0.8095 (pt0) cc_final: 0.7522 (pp30) REVERT: 2 356 SER cc_start: 0.8331 (m) cc_final: 0.7470 (p) REVERT: 2 520 TRP cc_start: 0.6397 (OUTLIER) cc_final: 0.5731 (p90) REVERT: 3 59 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7869 (ptm160) REVERT: 3 335 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8063 (ttp-110) REVERT: 3 363 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6499 (mm) REVERT: 3 520 ASN cc_start: 0.6761 (p0) cc_final: 0.6514 (p0) REVERT: 3 803 MET cc_start: 0.6699 (mmm) cc_final: 0.6312 (mmm) outliers start: 34 outliers final: 19 residues processed: 114 average time/residue: 0.4054 time to fit residues: 51.1517 Evaluate side-chains 107 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 520 TRP Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 236 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 385 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 117 optimal weight: 0.0060 chunk 73 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 110 optimal weight: 0.5980 chunk 135 optimal weight: 0.0020 chunk 36 optimal weight: 0.2980 chunk 139 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 168 GLN 3 232 GLN 3 341 ASN 3 473 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.206405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129816 restraints weight = 12557.897| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.70 r_work: 0.3204 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11012 Z= 0.113 Angle : 0.543 9.088 15096 Z= 0.273 Chirality : 0.042 0.185 1754 Planarity : 0.004 0.074 1972 Dihedral : 4.655 52.726 1649 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.61 % Allowed : 15.78 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 0.41 (0.22), residues: 1515 helix: 2.50 (0.20), residues: 678 sheet: -0.93 (0.43), residues: 141 loop : -1.87 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG 2 229 TYR 0.010 0.001 TYR 3 222 PHE 0.011 0.001 PHE 2 67 TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.001 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (10992) covalent geometry : angle 0.54289 / 0.27 (15054) SS BOND : bond 0.00184 / 0.10 ( 18) SS BOND : angle 0.64388 / 0.37 ( 36) hydrogen bonds : bond 0.03092 / 2.12 ( 548) hydrogen bonds : angle 3.64161 / 2.64 ( 1602) link_NAG-ASN : bond 0.00156 / 0.08 ( 2) link_NAG-ASN : angle 0.96606 / 0.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: 2 259 GLN cc_start: 0.8044 (pt0) cc_final: 0.7516 (pp30) REVERT: 2 356 SER cc_start: 0.8323 (m) cc_final: 0.7456 (p) REVERT: 3 183 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7211 (mtp85) REVERT: 3 335 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7930 (ttp-110) REVERT: 3 363 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6547 (mm) REVERT: 3 803 MET cc_start: 0.6632 (mmm) cc_final: 0.6183 (mmm) outliers start: 24 outliers final: 15 residues processed: 107 average time/residue: 0.4129 time to fit residues: 49.3291 Evaluate side-chains 105 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 29 optimal weight: 0.6980 chunk 136 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 137 optimal weight: 8.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 2 414 ASN 3 168 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN 3 341 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.205779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123294 restraints weight = 12619.328| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.69 r_work: 0.3198 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2939 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2939 r_free = 0.2939 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2939 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11012 Z= 0.168 Angle : 0.576 10.526 15096 Z= 0.288 Chirality : 0.043 0.205 1754 Planarity : 0.005 0.078 1972 Dihedral : 4.697 54.016 1649 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.50 % Allowed : 16.10 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 0.36 (0.22), residues: 1515 helix: 2.44 (0.20), residues: 683 sheet: -0.96 (0.43), residues: 142 loop : -1.91 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 2 229 TYR 0.011 0.001 TYR 2 165 PHE 0.014 0.002 PHE 2 327 TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.001 HIS 3 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (10992) covalent geometry : angle 0.57515 / 0.29 (15054) SS BOND : bond 0.00174 / 0.10 ( 18) SS BOND : angle 0.70204 / 0.41 ( 36) hydrogen bonds : bond 0.03430 / 2.33 ( 548) hydrogen bonds : angle 3.67298 / 2.67 ( 1602) link_NAG-ASN : bond 0.00082 / 0.04 ( 2) link_NAG-ASN : angle 0.95894 / 0.46 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7346 (mp0) REVERT: 2 259 GLN cc_start: 0.8118 (pt0) cc_final: 0.7516 (pp30) REVERT: 2 356 SER cc_start: 0.8271 (m) cc_final: 0.7398 (p) REVERT: 3 183 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7470 (mtp85) REVERT: 3 335 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8003 (ttp-110) REVERT: 3 363 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6676 (mm) REVERT: 3 520 ASN cc_start: 0.6805 (p0) cc_final: 0.6580 (p0) REVERT: 3 803 MET cc_start: 0.6673 (mmm) cc_final: 0.6235 (mmm) outliers start: 23 outliers final: 17 residues processed: 110 average time/residue: 0.3755 time to fit residues: 45.9961 Evaluate side-chains 109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 519 CYS Chi-restraints excluded: chain 2 residue 598 VAL Chi-restraints excluded: chain 3 residue 50 LYS Chi-restraints excluded: chain 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 232 ASN 3 232 GLN 3 251 ASN 3 341 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.205822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123249 restraints weight = 12784.714| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.68 r_work: 0.3189 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11012 Z= 0.169 Angle : 0.578 10.078 15096 Z= 0.289 Chirality : 0.043 0.193 1754 Planarity : 0.005 0.078 1972 Dihedral : 4.741 53.882 1649 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.50 % Allowed : 16.54 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 are not related in a simple way. whole: 0.34 (0.22), residues: 1515 helix: 2.43 (0.20), residues: 682 sheet: -0.95 (0.43), residues: 142 loop : -1.93 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 2 229 TYR 0.011 0.001 TYR 3 171 PHE 0.012 0.001 PHE 2 224 TRP 0.016 0.001 TRP 3 706 HIS 0.002 0.001 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (10992) covalent geometry : angle 0.57739 / 0.29 (15054) SS BOND : bond 0.00176 / 0.10 ( 18) SS BOND : angle 0.71339 / 0.40 ( 36) hydrogen bonds : bond 0.03430 / 2.32 ( 548) hydrogen bonds : angle 3.68636 / 2.68 ( 1602) link_NAG-ASN : bond 0.00095 / 0.05 ( 2) link_NAG-ASN : angle 0.98538 / 0.48 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3771.14 seconds wall clock time: 64 minutes 47.85 seconds (3887.85 seconds total)