Starting phenix.real_space_refine on Sat Nov 16 13:02:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/11_2024/8jcw_36167.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/11_2024/8jcw_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/11_2024/8jcw_36167.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/11_2024/8jcw_36167.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/11_2024/8jcw_36167.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcw_36167/11_2024/8jcw_36167.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.070 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 14, 'GLU:plan': 13, 'ARG:plan': 21} 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: {'GLN:plan1': 5, 'ARG:plan': 14, 'TYR:plan': 9, 'ASN:plan1': 12, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 12, 'GLU:plan': 12, 'ASP:plan': 11} 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.37, per 1000 atoms: 0.68 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: 2.96 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.24 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: 3.21 Time building geometry restraints manager: 3.38 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 - 34.72: 6571 34.72 - 69.45: 99 69.45 - 104.17: 17 104.17 - 138.89: 2 138.89 - 173.61: 2 Dihedral angle restraints: 6691 sinusoidal: 2260 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 6688 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.800 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 10992 Z= 0.219 Angle : 0.610 11.306 15054 Z= 0.295 Chirality : 0.168 4.866 1754 Planarity : 0.004 0.116 1972 Dihedral : 13.684 173.613 3771 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 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 TRP 0.032 0.001 TRP 3 706 HIS 0.002 0.000 HIS 2 87 PHE 0.012 0.001 PHE 3 544 TYR 0.008 0.001 TYR 3 563 ARG 0.004 0.000 ARG 3 183 *********************** 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 : 1.250 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: 1.0618 time to fit residues: 158.5576 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 : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 30.0000 chunk 115 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10992 Z= 0.363 Angle : 0.635 10.806 15054 Z= 0.319 Chirality : 0.045 0.223 1754 Planarity : 0.005 0.058 1972 Dihedral : 4.634 55.058 1845 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.39 % Allowed : 9.58 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1515 helix: 2.37 (0.20), residues: 678 sheet: -0.80 (0.42), residues: 138 loop : -1.82 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 3 706 HIS 0.003 0.001 HIS 2 396 PHE 0.016 0.002 PHE 2 327 TYR 0.016 0.002 TYR 3 171 ARG 0.008 0.001 ARG 3 253 *********************** 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 129 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: 2 259 GLN cc_start: 0.8060 (pt0) cc_final: 0.7750 (pp30) REVERT: 2 356 SER cc_start: 0.8279 (m) cc_final: 0.7692 (p) REVERT: 2 520 TRP cc_start: 0.6480 (OUTLIER) cc_final: 0.5941 (p90) REVERT: 3 59 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8000 (ptm160) REVERT: 3 183 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7117 (mtp85) REVERT: 3 328 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: 3 803 MET cc_start: 0.5854 (mmm) cc_final: 0.5516 (mmm) outliers start: 22 outliers final: 9 residues processed: 119 average time/residue: 1.0880 time to fit residues: 141.8771 Evaluate side-chains 109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 2 residue 520 TRP Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 60 ILE 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 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 168 GLN 3 232 GLN 3 251 ASN 3 470 ASN 3 508 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10992 Z= 0.265 Angle : 0.567 11.880 15054 Z= 0.285 Chirality : 0.043 0.184 1754 Planarity : 0.004 0.041 1972 Dihedral : 4.561 53.437 1845 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.16 % Allowed : 11.97 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.22), residues: 1515 helix: 2.32 (0.20), residues: 685 sheet: -0.92 (0.43), residues: 137 loop : -1.83 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 706 HIS 0.002 0.001 HIS 3 94 PHE 0.012 0.002 PHE 2 224 TYR 0.012 0.001 TYR 3 171 ARG 0.011 0.000 ARG 2 229 *********************** 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 124 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: 2 65 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: 2 227 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: 2 259 GLN cc_start: 0.8023 (pt0) cc_final: 0.7747 (pp30) REVERT: 2 356 SER cc_start: 0.8300 (m) cc_final: 0.7654 (p) REVERT: 2 520 TRP cc_start: 0.6482 (OUTLIER) cc_final: 0.5799 (p90) REVERT: 3 59 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8004 (ptm160) REVERT: 3 183 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7065 (mtp85) REVERT: 3 520 ASN cc_start: 0.6876 (p0) cc_final: 0.6620 (p0) REVERT: 3 803 MET cc_start: 0.5893 (mmm) cc_final: 0.5516 (mmm) outliers start: 29 outliers final: 15 residues processed: 112 average time/residue: 0.9643 time to fit residues: 119.7218 Evaluate side-chains 110 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 520 TRP 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 177 LYS 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 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 136 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 168 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN 3 344 ASN 3 472 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 10992 Z= 0.497 Angle : 0.707 15.207 15054 Z= 0.353 Chirality : 0.048 0.226 1754 Planarity : 0.005 0.051 1972 Dihedral : 5.354 57.490 1845 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 4.03 % Allowed : 13.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1515 helix: 2.00 (0.20), residues: 689 sheet: -1.29 (0.41), residues: 147 loop : -2.03 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 3 706 HIS 0.004 0.001 HIS 3 94 PHE 0.018 0.002 PHE 3 195 TYR 0.017 0.002 TYR 3 171 ARG 0.010 0.001 ARG 2 229 *********************** 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 134 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: 2 154 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9009 (tm) REVERT: 2 227 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: 2 259 GLN cc_start: 0.8073 (pt0) cc_final: 0.7740 (pp30) REVERT: 2 356 SER cc_start: 0.8350 (m) cc_final: 0.7672 (p) REVERT: 2 485 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7828 (mt) REVERT: 2 520 TRP cc_start: 0.6383 (OUTLIER) cc_final: 0.5417 (p90) REVERT: 3 520 ASN cc_start: 0.7089 (p0) cc_final: 0.6764 (p0) REVERT: 3 803 MET cc_start: 0.5948 (mmm) cc_final: 0.5547 (mmm) outliers start: 37 outliers final: 21 residues processed: 122 average time/residue: 0.9548 time to fit residues: 129.3045 Evaluate side-chains 116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 139 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 267 VAL 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 485 ILE Chi-restraints excluded: chain 2 residue 518 CYS Chi-restraints excluded: chain 2 residue 520 TRP 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 177 LYS 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 385 GLU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 518 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 2 414 ASN 3 168 GLN 3 232 GLN 3 251 ASN 3 344 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10992 Z= 0.219 Angle : 0.564 13.497 15054 Z= 0.282 Chirality : 0.042 0.189 1754 Planarity : 0.004 0.067 1972 Dihedral : 4.866 53.788 1845 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 3.92 % Allowed : 14.04 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1515 helix: 2.24 (0.21), residues: 685 sheet: -1.11 (0.42), residues: 143 loop : -1.94 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.012 0.001 PHE 2 67 TYR 0.010 0.001 TYR 3 171 ARG 0.011 0.000 ARG 2 229 *********************** 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 128 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: 2 259 GLN cc_start: 0.7985 (pt0) cc_final: 0.7697 (pp30) REVERT: 2 356 SER cc_start: 0.8395 (m) cc_final: 0.7693 (p) REVERT: 2 520 TRP cc_start: 0.6512 (OUTLIER) cc_final: 0.5732 (p90) REVERT: 3 59 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7999 (ptm160) REVERT: 3 72 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7118 (ttt) REVERT: 3 183 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.6989 (mtp85) REVERT: 3 363 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6698 (mm) REVERT: 3 803 MET cc_start: 0.5947 (mmm) cc_final: 0.5528 (mmm) outliers start: 36 outliers final: 19 residues processed: 117 average time/residue: 0.9657 time to fit residues: 125.4637 Evaluate side-chains 109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 50 CYS Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 154 LEU Chi-restraints excluded: chain 2 residue 221 ILE 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 520 TRP Chi-restraints excluded: chain 2 residue 597 VAL Chi-restraints excluded: chain 3 residue 50 LYS 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 346 HIS Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 438 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 29 optimal weight: 0.0040 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 40.0000 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 344 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10992 Z= 0.198 Angle : 0.555 15.344 15054 Z= 0.275 Chirality : 0.042 0.188 1754 Planarity : 0.004 0.068 1972 Dihedral : 4.594 53.324 1845 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.81 % Allowed : 14.15 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1515 helix: 2.40 (0.20), residues: 679 sheet: -0.90 (0.43), residues: 142 loop : -1.92 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.012 0.001 PHE 3 195 TYR 0.009 0.001 TYR 3 171 ARG 0.013 0.000 ARG 2 229 *********************** 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 129 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: 2 259 GLN cc_start: 0.8011 (pt0) cc_final: 0.7714 (pp30) REVERT: 2 356 SER cc_start: 0.8388 (m) cc_final: 0.7672 (p) REVERT: 2 520 TRP cc_start: 0.6631 (OUTLIER) cc_final: 0.5815 (p90) REVERT: 3 72 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7079 (ttt) REVERT: 3 183 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7037 (mtp85) REVERT: 3 363 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6738 (mm) REVERT: 3 803 MET cc_start: 0.5941 (mmm) cc_final: 0.5500 (mmm) outliers start: 35 outliers final: 22 residues processed: 119 average time/residue: 0.9588 time to fit residues: 126.4703 Evaluate side-chains 113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 50 CYS 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 221 ILE 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 520 TRP Chi-restraints excluded: chain 3 residue 50 LYS 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 177 LYS 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 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 Chi-restraints excluded: chain 3 residue 438 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10992 Z= 0.304 Angle : 0.606 18.462 15054 Z= 0.299 Chirality : 0.044 0.197 1754 Planarity : 0.005 0.074 1972 Dihedral : 4.779 53.517 1845 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.92 % Allowed : 15.34 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1515 helix: 2.34 (0.20), residues: 679 sheet: -0.91 (0.43), residues: 142 loop : -1.95 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.001 HIS 2 365 PHE 0.016 0.002 PHE 2 327 TYR 0.012 0.001 TYR 3 171 ARG 0.015 0.000 ARG 2 229 *********************** 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 122 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: 2 259 GLN cc_start: 0.8068 (pt0) cc_final: 0.7726 (pp30) REVERT: 2 356 SER cc_start: 0.8387 (m) cc_final: 0.7624 (p) REVERT: 2 520 TRP cc_start: 0.6408 (OUTLIER) cc_final: 0.5546 (p90) REVERT: 3 183 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.6976 (mtp85) REVERT: 3 328 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: 3 363 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6768 (mm) REVERT: 3 520 ASN cc_start: 0.7016 (p0) cc_final: 0.6694 (p0) REVERT: 3 803 MET cc_start: 0.5959 (mmm) cc_final: 0.5512 (mmm) outliers start: 36 outliers final: 23 residues processed: 113 average time/residue: 1.0426 time to fit residues: 130.3130 Evaluate side-chains 112 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 50 CYS 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 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 489 SER 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 3 residue 60 ILE Chi-restraints excluded: chain 3 residue 140 LEU 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 236 LEU Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 3 residue 328 GLN 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 Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 168 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 341 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10992 Z= 0.220 Angle : 0.575 16.790 15054 Z= 0.284 Chirality : 0.042 0.221 1754 Planarity : 0.005 0.067 1972 Dihedral : 4.648 52.986 1845 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.13 % Allowed : 15.56 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1515 helix: 2.41 (0.20), residues: 679 sheet: -0.91 (0.43), residues: 143 loop : -1.89 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.013 0.001 PHE 3 195 TYR 0.011 0.001 TYR 3 171 ARG 0.016 0.001 ARG 2 229 *********************** 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 126 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: 2 259 GLN cc_start: 0.8092 (pt0) cc_final: 0.7761 (pp30) REVERT: 2 356 SER cc_start: 0.8470 (m) cc_final: 0.7691 (p) REVERT: 2 520 TRP cc_start: 0.6517 (OUTLIER) cc_final: 0.5704 (p90) REVERT: 3 72 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7103 (ttt) REVERT: 3 183 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.6974 (mtp85) REVERT: 3 328 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7310 (pt0) REVERT: 3 363 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6792 (mm) REVERT: 3 520 ASN cc_start: 0.7007 (p0) cc_final: 0.6668 (p0) REVERT: 3 803 MET cc_start: 0.6007 (mmm) cc_final: 0.5551 (mmm) outliers start: 38 outliers final: 25 residues processed: 117 average time/residue: 0.9302 time to fit residues: 121.0503 Evaluate side-chains 118 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 50 CYS 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 221 ILE 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 489 SER 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 597 VAL Chi-restraints excluded: chain 2 residue 598 VAL 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 177 LYS 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 328 GLN 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 Chi-restraints excluded: chain 3 residue 438 ILE 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 128 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 168 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 251 ASN 3 341 ASN 3 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 10992 Z= 0.587 Angle : 0.745 19.245 15054 Z= 0.368 Chirality : 0.049 0.199 1754 Planarity : 0.006 0.083 1972 Dihedral : 5.519 58.365 1845 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.00 % Favored : 92.87 % Rotamer: Outliers : 3.92 % Allowed : 16.10 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1515 helix: 2.06 (0.21), residues: 685 sheet: -1.24 (0.42), residues: 142 loop : -2.11 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 3 303 HIS 0.003 0.001 HIS 2 365 PHE 0.021 0.002 PHE 3 195 TYR 0.022 0.002 TYR 3 186 ARG 0.014 0.001 ARG 2 229 *********************** 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 121 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 85 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: 2 154 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.9023 (tm) REVERT: 2 227 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: 2 259 GLN cc_start: 0.8169 (pt0) cc_final: 0.7682 (pp30) REVERT: 2 356 SER cc_start: 0.8404 (m) cc_final: 0.7659 (p) REVERT: 2 485 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7934 (mt) REVERT: 2 520 TRP cc_start: 0.6242 (OUTLIER) cc_final: 0.5219 (p90) REVERT: 3 72 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7322 (ttt) REVERT: 3 328 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: 3 363 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6581 (mm) REVERT: 3 520 ASN cc_start: 0.7027 (p0) cc_final: 0.6691 (p0) REVERT: 3 803 MET cc_start: 0.6015 (mmm) cc_final: 0.5612 (mmm) outliers start: 36 outliers final: 23 residues processed: 114 average time/residue: 1.1024 time to fit residues: 138.1578 Evaluate side-chains 113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 50 CYS 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 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 485 ILE Chi-restraints excluded: chain 2 residue 489 SER 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 597 VAL Chi-restraints excluded: chain 2 residue 598 VAL 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 316 VAL Chi-restraints excluded: chain 3 residue 328 GLN 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 422 MET Chi-restraints excluded: chain 3 residue 438 ILE 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 88 optimal weight: 0.3980 chunk 68 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 168 GLN 3 232 GLN 3 341 ASN 3 386 GLN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10992 Z= 0.227 Angle : 0.600 17.404 15054 Z= 0.297 Chirality : 0.043 0.205 1754 Planarity : 0.005 0.077 1972 Dihedral : 4.999 53.440 1845 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.26 % Allowed : 17.30 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1515 helix: 2.33 (0.21), residues: 679 sheet: -1.26 (0.42), residues: 149 loop : -1.94 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 706 HIS 0.002 0.000 HIS 3 485 PHE 0.012 0.001 PHE 2 67 TYR 0.011 0.001 TYR 3 171 ARG 0.018 0.001 ARG 2 229 ********************** 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 115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: 2 227 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: 2 259 GLN cc_start: 0.8075 (pt0) cc_final: 0.7643 (pp30) REVERT: 2 356 SER cc_start: 0.8372 (m) cc_final: 0.7617 (p) REVERT: 2 520 TRP cc_start: 0.6508 (OUTLIER) cc_final: 0.5593 (p90) REVERT: 3 72 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7137 (ttt) REVERT: 3 183 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.6953 (mtp85) REVERT: 3 328 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: 3 363 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6723 (mm) REVERT: 3 520 ASN cc_start: 0.7005 (p0) cc_final: 0.6645 (p0) REVERT: 3 803 MET cc_start: 0.5961 (mmm) cc_final: 0.5507 (mmm) outliers start: 30 outliers final: 22 residues processed: 108 average time/residue: 1.0080 time to fit residues: 120.3154 Evaluate side-chains 112 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 50 CYS 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 367 LEU Chi-restraints excluded: chain 2 residue 400 CYS Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 485 ILE Chi-restraints excluded: chain 2 residue 489 SER 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 597 VAL Chi-restraints excluded: chain 2 residue 598 VAL 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 328 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.0070 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 232 ASN 3 168 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN 3 341 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.203804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121526 restraints weight = 12652.454| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.05 r_work: 0.3196 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10992 Z= 0.325 Angle : 0.634 18.532 15054 Z= 0.312 Chirality : 0.044 0.192 1754 Planarity : 0.005 0.077 1972 Dihedral : 5.054 53.558 1845 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.06 % Favored : 92.87 % Rotamer: Outliers : 3.48 % Allowed : 17.30 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1515 helix: 2.27 (0.21), residues: 683 sheet: -1.05 (0.43), residues: 142 loop : -1.99 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 706 HIS 0.002 0.001 HIS 2 365 PHE 0.017 0.002 PHE 3 195 TYR 0.013 0.002 TYR 3 171 ARG 0.021 0.001 ARG 3 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3438.61 seconds wall clock time: 62 minutes 36.49 seconds (3756.49 seconds total)