Starting phenix.real_space_refine on Tue Mar 3 22:02:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjf_51390/03_2026/9gjf_51390.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjf_51390/03_2026/9gjf_51390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gjf_51390/03_2026/9gjf_51390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjf_51390/03_2026/9gjf_51390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gjf_51390/03_2026/9gjf_51390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjf_51390/03_2026/9gjf_51390.map" } resolution = 3.1 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= 0.003 sd= 0.131 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 87 5.16 5 C 5375 2.51 5 N 1453 2.21 5 O 1756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8671 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 6237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6237 Classifications: {'peptide': 796} Link IDs: {'PTRANS': 20, 'TRANS': 775} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.21, per 1000 atoms: 0.25 Number of scatterers: 8671 At special positions: 0 Unit cell: (90.688, 113.984, 113.984, 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 87 16.00 O 1756 8.00 N 1453 7.00 C 5375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.02 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.03 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.04 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS H 653 " - pdb=" SG CYS H 697 " distance=2.03 Simple disulfide: pdb=" SG CYS H 672 " - pdb=" SG CYS H 702 " distance=2.03 Simple disulfide: pdb=" SG CYS H 689 " - pdb=" SG CYS H 718 " distance=2.03 Simple disulfide: pdb=" SG CYS H 715 " - pdb=" SG CYS H 746 " distance=2.03 Simple disulfide: pdb=" SG CYS H 732 " - pdb=" SG CYS H 756 " distance=2.03 Simple disulfide: pdb=" SG CYS H 739 " - pdb=" SG CYS H 775 " distance=2.03 Simple disulfide: pdb=" SG CYS H 772 " - pdb=" SG CYS H 798 " distance=2.03 Simple disulfide: pdb=" SG CYS H 780 " - pdb=" SG CYS H 811 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN H 337 " " NAG B 1 " - " ASN H 390 " " NAG H 901 " - " ASN H 468 " " NAG H 902 " - " ASN H 198 " " NAG H 903 " - " ASN H 659 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 304.1 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 26 sheets defined 16.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'H' and resid 30 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.813A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 122 Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 188 through 196 removed outlier: 4.109A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.516A pdb=" N LEU H 241 " --> pdb=" O LEU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 273 removed outlier: 3.503A pdb=" N VAL H 273 " --> pdb=" O TYR H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 299 Processing helix chain 'H' and resid 328 through 333 Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.625A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 361 No H-bonds generated for 'chain 'H' and resid 359 through 361' Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 372 through 374 No H-bonds generated for 'chain 'H' and resid 372 through 374' Processing helix chain 'H' and resid 375 through 391 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 586 through 590 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'H' and resid 684 through 690 removed outlier: 3.661A pdb=" N MET H 688 " --> pdb=" O LYS H 684 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS H 690 " --> pdb=" O GLU H 686 " (cutoff:3.500A) Processing helix chain 'H' and resid 767 through 773 Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.772A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 removed outlier: 3.661A pdb=" N PHE L 139 " --> pdb=" O GLU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 Processing helix chain 'L' and resid 278 through 281 Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.838A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY H 36 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP H 29 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.838A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 257 through 262 removed outlier: 6.449A pdb=" N THR H 214 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY H 246 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU H 252 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA H 217 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU H 318 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE H 219 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 456 removed outlier: 6.934A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL H 463 " --> pdb=" O GLU H 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA8, first strand: chain 'H' and resid 511 through 515 removed outlier: 6.509A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 540 through 544 Processing sheet with id=AB1, first strand: chain 'H' and resid 569 through 573 removed outlier: 3.658A pdb=" N GLU H 581 " --> pdb=" O LYS H 572 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 601 through 602 removed outlier: 3.971A pdb=" N LYS H 602 " --> pdb=" O GLN H 612 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN H 612 " --> pdb=" O LYS H 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 628 through 630 Processing sheet with id=AB4, first strand: chain 'H' and resid 650 through 651 Processing sheet with id=AB5, first strand: chain 'H' and resid 693 through 698 Processing sheet with id=AB6, first strand: chain 'H' and resid 717 through 720 Processing sheet with id=AB7, first strand: chain 'H' and resid 744 through 749 removed outlier: 3.581A pdb=" N GLY H 749 " --> pdb=" O SER H 753 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 787 through 791 Processing sheet with id=AB9, first strand: chain 'H' and resid 809 through 812 Processing sheet with id=AC1, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.284A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AC3, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AC4, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AC5, first strand: chain 'L' and resid 124 through 125 removed outlier: 4.823A pdb=" N GLN L 124 " --> pdb=" O ILE L 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 124 through 125 removed outlier: 4.823A pdb=" N GLN L 124 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA L 168 " --> pdb=" O ALA L 271 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE L 269 " --> pdb=" O LEU L 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 191 through 192 Processing sheet with id=AC8, first strand: chain 'L' and resid 207 through 212 245 hydrogen bonds defined for protein. 618 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: 1.71 Time building geometry restraints manager: 1.13 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: 2795 1.34 - 1.46: 2117 1.46 - 1.58: 3826 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 8843 Sorted by residual: bond pdb=" N ILE H 338 " pdb=" CA ILE H 338 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.19e-02 7.06e+03 9.07e+00 bond pdb=" N LYS H 336 " pdb=" CA LYS H 336 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.32e-02 5.74e+03 5.71e+00 bond pdb=" N ASN H 337 " pdb=" CA ASN H 337 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.46e-02 4.69e+03 3.45e+00 bond pdb=" C ASN H 337 " pdb=" O ASN H 337 " ideal model delta sigma weight residual 1.233 1.248 -0.015 1.30e-02 5.92e+03 1.28e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 8838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11772 1.49 - 2.98: 152 2.98 - 4.46: 25 4.46 - 5.95: 10 5.95 - 7.44: 1 Bond angle restraints: 11960 Sorted by residual: angle pdb=" C ASN H 337 " pdb=" CA ASN H 337 " pdb=" CB ASN H 337 " ideal model delta sigma weight residual 111.86 119.30 -7.44 1.34e+00 5.57e-01 3.08e+01 angle pdb=" CA ASN H 337 " pdb=" C ASN H 337 " pdb=" O ASN H 337 " ideal model delta sigma weight residual 121.65 117.79 3.86 1.17e+00 7.31e-01 1.09e+01 angle pdb=" N LYS H 336 " pdb=" CA LYS H 336 " pdb=" C LYS H 336 " ideal model delta sigma weight residual 113.16 109.31 3.85 1.24e+00 6.50e-01 9.66e+00 angle pdb=" N ASN H 337 " pdb=" CA ASN H 337 " pdb=" C ASN H 337 " ideal model delta sigma weight residual 111.52 107.67 3.85 1.40e+00 5.10e-01 7.55e+00 angle pdb=" CA GLN H 638 " pdb=" CB GLN H 638 " pdb=" CG GLN H 638 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.24e+00 ... (remaining 11955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4869 17.62 - 35.23: 548 35.23 - 52.85: 144 52.85 - 70.47: 46 70.47 - 88.08: 17 Dihedral angle restraints: 5624 sinusoidal: 2458 harmonic: 3166 Sorted by residual: dihedral pdb=" CB CYS H 592 " pdb=" SG CYS H 592 " pdb=" SG CYS H 630 " pdb=" CB CYS H 630 " ideal model delta sinusoidal sigma weight residual -86.00 -155.19 69.19 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS H 477 " pdb=" SG CYS H 477 " pdb=" SG CYS H 515 " pdb=" CB CYS H 515 " ideal model delta sinusoidal sigma weight residual 93.00 35.73 57.27 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS H 420 " pdb=" SG CYS H 420 " pdb=" SG CYS H 456 " pdb=" CB CYS H 456 " ideal model delta sinusoidal sigma weight residual 93.00 146.82 -53.82 1 1.00e+01 1.00e-02 3.93e+01 ... (remaining 5621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1228 0.082 - 0.164: 105 0.164 - 0.247: 2 0.247 - 0.329: 1 0.329 - 0.411: 2 Chirality restraints: 1338 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.23e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN H 337 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 1335 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.195 2.00e-02 2.50e+03 1.62e-01 3.29e+02 pdb=" C7 NAG B 1 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.139 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.267 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN H 468 " 0.141 2.00e-02 2.50e+03 1.47e-01 2.70e+02 pdb=" CG ASN H 468 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN H 468 " -0.077 2.00e-02 2.50e+03 pdb=" ND2 ASN H 468 " -0.201 2.00e-02 2.50e+03 pdb=" C1 NAG H 901 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 469 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" CG ASP H 469 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP H 469 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP H 469 " -0.011 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 23 2.44 - 3.05: 5201 3.05 - 3.67: 12219 3.67 - 4.28: 19079 4.28 - 4.90: 32554 Nonbonded interactions: 69076 Sorted by model distance: nonbonded pdb=" OD2 ASP H 334 " pdb=" O2 BMA B 3 " model vdw 1.820 3.040 nonbonded pdb=" OD1 ASN H 468 " pdb=" C1 NAG H 901 " model vdw 2.262 2.776 nonbonded pdb=" NZ LYS H 748 " pdb=" OD1 ASN H 752 " model vdw 2.294 3.120 nonbonded pdb=" OE2 GLU H 646 " pdb=" OG1 THR H 665 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU H 20 " pdb=" OG SER H 45 " model vdw 2.306 3.040 ... (remaining 69071 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.002 0.042 8890 Z= 0.119 Angle : 0.555 23.462 12067 Z= 0.275 Chirality : 0.045 0.411 1338 Planarity : 0.005 0.162 1530 Dihedral : 16.603 88.085 3492 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.21 % Allowed : 16.99 % Favored : 82.80 % 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: 0.19 (0.26), residues: 1065 helix: -0.23 (0.51), residues: 110 sheet: 0.46 (0.32), residues: 248 loop : 0.15 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 650 TYR 0.010 0.001 TYR L 53 PHE 0.010 0.001 PHE H 64 TRP 0.006 0.001 TRP L 223 HIS 0.002 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8843) covalent geometry : angle 0.47122 (11960) SS BOND : bond 0.00216 ( 34) SS BOND : angle 0.81695 ( 68) hydrogen bonds : bond 0.22918 ( 219) hydrogen bonds : angle 8.65367 ( 618) link_ALPHA1-2 : bond 0.00393 ( 2) link_ALPHA1-2 : angle 1.36511 ( 6) link_ALPHA1-3 : bond 0.00349 ( 1) link_ALPHA1-3 : angle 1.41002 ( 3) link_ALPHA1-6 : bond 0.00389 ( 1) link_ALPHA1-6 : angle 1.39869 ( 3) link_BETA1-4 : bond 0.00923 ( 4) link_BETA1-4 : angle 3.39631 ( 12) link_NAG-ASN : bond 0.02683 ( 5) link_NAG-ASN : angle 7.56785 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.346 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 93 average time/residue: 0.1346 time to fit residues: 16.3038 Evaluate side-chains 91 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 612 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.166014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.112154 restraints weight = 9447.952| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.21 r_work: 0.2929 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8890 Z= 0.126 Angle : 0.529 6.577 12067 Z= 0.274 Chirality : 0.045 0.275 1338 Planarity : 0.004 0.038 1530 Dihedral : 8.391 67.567 1442 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.18 % Allowed : 15.23 % Favored : 82.59 % 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: 0.15 (0.26), residues: 1065 helix: -0.28 (0.49), residues: 116 sheet: 0.37 (0.32), residues: 264 loop : 0.16 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 650 TYR 0.021 0.001 TYR H 27 PHE 0.013 0.001 PHE H 258 TRP 0.016 0.001 TRP H 66 HIS 0.002 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8843) covalent geometry : angle 0.50824 (11960) SS BOND : bond 0.00275 ( 34) SS BOND : angle 0.96445 ( 68) hydrogen bonds : bond 0.04050 ( 219) hydrogen bonds : angle 6.02828 ( 618) link_ALPHA1-2 : bond 0.00430 ( 2) link_ALPHA1-2 : angle 1.34885 ( 6) link_ALPHA1-3 : bond 0.00635 ( 1) link_ALPHA1-3 : angle 1.37436 ( 3) link_ALPHA1-6 : bond 0.00407 ( 1) link_ALPHA1-6 : angle 1.69017 ( 3) link_BETA1-4 : bond 0.00632 ( 4) link_BETA1-4 : angle 3.09151 ( 12) link_NAG-ASN : bond 0.00280 ( 5) link_NAG-ASN : angle 2.40609 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.376 Fit side-chains REVERT: H 232 GLN cc_start: 0.7232 (mp10) cc_final: 0.7019 (mt0) REVERT: H 251 TYR cc_start: 0.7407 (m-80) cc_final: 0.7092 (m-80) REVERT: H 638 GLN cc_start: 0.7303 (pm20) cc_final: 0.6956 (tp40) REVERT: H 646 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7255 (pt0) outliers start: 21 outliers final: 10 residues processed: 114 average time/residue: 0.1091 time to fit residues: 16.7199 Evaluate side-chains 97 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 597 THR Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain L residue 35 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 92 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN H 232 GLN H 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.166330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110120 restraints weight = 9305.391| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.34 r_work: 0.2902 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8890 Z= 0.108 Angle : 0.497 6.077 12067 Z= 0.258 Chirality : 0.044 0.220 1338 Planarity : 0.003 0.039 1530 Dihedral : 6.759 61.004 1439 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.28 % Allowed : 15.03 % Favored : 82.69 % 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: 0.24 (0.26), residues: 1065 helix: -0.33 (0.48), residues: 122 sheet: 0.56 (0.32), residues: 254 loop : 0.19 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 650 TYR 0.018 0.001 TYR H 27 PHE 0.013 0.001 PHE H 258 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS H 341 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8843) covalent geometry : angle 0.47910 (11960) SS BOND : bond 0.00225 ( 34) SS BOND : angle 0.88106 ( 68) hydrogen bonds : bond 0.03339 ( 219) hydrogen bonds : angle 5.46386 ( 618) link_ALPHA1-2 : bond 0.00347 ( 2) link_ALPHA1-2 : angle 1.40753 ( 6) link_ALPHA1-3 : bond 0.00908 ( 1) link_ALPHA1-3 : angle 1.43344 ( 3) link_ALPHA1-6 : bond 0.00205 ( 1) link_ALPHA1-6 : angle 1.65871 ( 3) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 2.88788 ( 12) link_NAG-ASN : bond 0.00228 ( 5) link_NAG-ASN : angle 1.92223 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.229 Fit side-chains REVERT: H 251 TYR cc_start: 0.7300 (m-80) cc_final: 0.6911 (m-80) REVERT: H 638 GLN cc_start: 0.7203 (pm20) cc_final: 0.6689 (pm20) REVERT: L 51 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: L 107 MET cc_start: 0.9370 (mmt) cc_final: 0.8825 (mmt) outliers start: 22 outliers final: 10 residues processed: 113 average time/residue: 0.1078 time to fit residues: 16.1475 Evaluate side-chains 100 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0270 chunk 94 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 0.0570 chunk 14 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.116317 restraints weight = 9528.012| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.23 r_work: 0.2962 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8890 Z= 0.086 Angle : 0.482 6.056 12067 Z= 0.251 Chirality : 0.043 0.219 1338 Planarity : 0.003 0.036 1530 Dihedral : 6.295 55.474 1439 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 2.07 % Allowed : 16.17 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.26), residues: 1065 helix: -0.19 (0.51), residues: 116 sheet: 0.51 (0.32), residues: 252 loop : 0.23 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 650 TYR 0.014 0.001 TYR H 27 PHE 0.013 0.001 PHE H 258 TRP 0.010 0.001 TRP H 66 HIS 0.004 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 8843) covalent geometry : angle 0.46572 (11960) SS BOND : bond 0.00205 ( 34) SS BOND : angle 0.91791 ( 68) hydrogen bonds : bond 0.02925 ( 219) hydrogen bonds : angle 5.18350 ( 618) link_ALPHA1-2 : bond 0.00354 ( 2) link_ALPHA1-2 : angle 1.43507 ( 6) link_ALPHA1-3 : bond 0.01099 ( 1) link_ALPHA1-3 : angle 1.38845 ( 3) link_ALPHA1-6 : bond 0.00341 ( 1) link_ALPHA1-6 : angle 1.62578 ( 3) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 2.66747 ( 12) link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 1.73983 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: H 232 GLN cc_start: 0.6977 (mt0) cc_final: 0.6651 (mt0) REVERT: H 251 TYR cc_start: 0.7279 (m-80) cc_final: 0.6923 (m-80) REVERT: H 266 GLN cc_start: 0.7928 (mm110) cc_final: 0.7679 (mm-40) REVERT: H 319 MET cc_start: 0.9044 (mtp) cc_final: 0.8764 (mtm) REVERT: H 507 ASP cc_start: 0.8343 (t0) cc_final: 0.8086 (t0) REVERT: H 638 GLN cc_start: 0.7242 (pm20) cc_final: 0.6729 (pm20) REVERT: H 646 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: L 20 ASP cc_start: 0.8553 (p0) cc_final: 0.8246 (p0) REVERT: L 51 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.7737 (pm20) outliers start: 20 outliers final: 12 residues processed: 113 average time/residue: 0.1161 time to fit residues: 17.6209 Evaluate side-chains 105 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 412 CYS Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 0.0980 chunk 99 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN H 627 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.161234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103365 restraints weight = 9424.230| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.40 r_work: 0.2915 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 8890 Z= 0.274 Angle : 0.620 7.229 12067 Z= 0.322 Chirality : 0.049 0.205 1338 Planarity : 0.004 0.043 1530 Dihedral : 6.825 57.221 1439 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 3.11 % Allowed : 15.54 % Favored : 81.35 % 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: -0.09 (0.25), residues: 1065 helix: -0.60 (0.47), residues: 121 sheet: 0.24 (0.31), residues: 264 loop : 0.01 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 650 TYR 0.029 0.002 TYR H 27 PHE 0.018 0.002 PHE H 64 TRP 0.014 0.002 TRP H 435 HIS 0.004 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00670 ( 8843) covalent geometry : angle 0.60027 (11960) SS BOND : bond 0.00443 ( 34) SS BOND : angle 1.38768 ( 68) hydrogen bonds : bond 0.03778 ( 219) hydrogen bonds : angle 5.61646 ( 618) link_ALPHA1-2 : bond 0.00254 ( 2) link_ALPHA1-2 : angle 1.41776 ( 6) link_ALPHA1-3 : bond 0.00642 ( 1) link_ALPHA1-3 : angle 2.03904 ( 3) link_ALPHA1-6 : bond 0.00377 ( 1) link_ALPHA1-6 : angle 1.61859 ( 3) link_BETA1-4 : bond 0.00553 ( 4) link_BETA1-4 : angle 2.88654 ( 12) link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 2.10523 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: H 25 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8841 (pt) REVERT: H 251 TYR cc_start: 0.7611 (m-80) cc_final: 0.7304 (m-80) REVERT: H 507 ASP cc_start: 0.8357 (t0) cc_final: 0.8118 (t0) REVERT: H 638 GLN cc_start: 0.7313 (pm20) cc_final: 0.6781 (pm20) REVERT: H 646 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7428 (pt0) outliers start: 30 outliers final: 20 residues processed: 113 average time/residue: 0.1057 time to fit residues: 15.8595 Evaluate side-chains 107 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 226 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 450 CYS Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 757 VAL Chi-restraints excluded: chain L residue 35 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105023 restraints weight = 9381.657| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.32 r_work: 0.2851 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8890 Z= 0.188 Angle : 0.558 6.636 12067 Z= 0.291 Chirality : 0.046 0.199 1338 Planarity : 0.004 0.044 1530 Dihedral : 6.512 51.719 1439 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 2.69 % Allowed : 16.17 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.07 (0.25), residues: 1065 helix: -0.57 (0.48), residues: 121 sheet: 0.41 (0.32), residues: 243 loop : -0.05 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 650 TYR 0.023 0.001 TYR H 27 PHE 0.017 0.002 PHE H 64 TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8843) covalent geometry : angle 0.53996 (11960) SS BOND : bond 0.00368 ( 34) SS BOND : angle 1.16887 ( 68) hydrogen bonds : bond 0.03397 ( 219) hydrogen bonds : angle 5.49967 ( 618) link_ALPHA1-2 : bond 0.00324 ( 2) link_ALPHA1-2 : angle 1.46190 ( 6) link_ALPHA1-3 : bond 0.00838 ( 1) link_ALPHA1-3 : angle 1.96068 ( 3) link_ALPHA1-6 : bond 0.00253 ( 1) link_ALPHA1-6 : angle 1.72286 ( 3) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 2.73073 ( 12) link_NAG-ASN : bond 0.00160 ( 5) link_NAG-ASN : angle 1.96904 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.296 Fit side-chains REVERT: H 25 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8796 (pt) REVERT: H 251 TYR cc_start: 0.7561 (m-80) cc_final: 0.7288 (m-80) REVERT: H 507 ASP cc_start: 0.8369 (t0) cc_final: 0.7983 (t0) REVERT: H 638 GLN cc_start: 0.7306 (pm20) cc_final: 0.6763 (pm20) REVERT: H 646 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: H 701 LYS cc_start: 0.7019 (mttt) cc_final: 0.6781 (mmmm) outliers start: 26 outliers final: 17 residues processed: 108 average time/residue: 0.1041 time to fit residues: 15.0600 Evaluate side-chains 103 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 58 MET Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 809 SER Chi-restraints excluded: chain L residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN H 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104451 restraints weight = 9422.560| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.10 r_work: 0.2931 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8890 Z= 0.173 Angle : 0.547 6.646 12067 Z= 0.285 Chirality : 0.046 0.195 1338 Planarity : 0.004 0.044 1530 Dihedral : 6.306 47.874 1439 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 2.59 % Allowed : 16.58 % Favored : 80.83 % 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: -0.11 (0.25), residues: 1065 helix: -0.62 (0.47), residues: 122 sheet: 0.35 (0.32), residues: 252 loop : -0.05 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 650 TYR 0.022 0.001 TYR H 27 PHE 0.016 0.002 PHE H 64 TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8843) covalent geometry : angle 0.52962 (11960) SS BOND : bond 0.00328 ( 34) SS BOND : angle 1.13434 ( 68) hydrogen bonds : bond 0.03290 ( 219) hydrogen bonds : angle 5.40959 ( 618) link_ALPHA1-2 : bond 0.00340 ( 2) link_ALPHA1-2 : angle 1.48176 ( 6) link_ALPHA1-3 : bond 0.00874 ( 1) link_ALPHA1-3 : angle 1.99481 ( 3) link_ALPHA1-6 : bond 0.00249 ( 1) link_ALPHA1-6 : angle 1.75751 ( 3) link_BETA1-4 : bond 0.00538 ( 4) link_BETA1-4 : angle 2.60758 ( 12) link_NAG-ASN : bond 0.00155 ( 5) link_NAG-ASN : angle 1.91627 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.304 Fit side-chains REVERT: H 251 TYR cc_start: 0.7571 (m-80) cc_final: 0.7343 (m-80) REVERT: H 507 ASP cc_start: 0.8323 (t0) cc_final: 0.7984 (t0) REVERT: H 638 GLN cc_start: 0.7271 (pm20) cc_final: 0.6698 (pm20) REVERT: H 646 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: H 701 LYS cc_start: 0.7062 (mttt) cc_final: 0.6808 (mmmm) REVERT: L 94 GLU cc_start: 0.8162 (mp0) cc_final: 0.7890 (mp0) outliers start: 25 outliers final: 19 residues processed: 108 average time/residue: 0.1191 time to fit residues: 16.8908 Evaluate side-chains 102 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 133 ASP Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 575 LEU Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 809 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN H 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.164631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109018 restraints weight = 9272.907| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.30 r_work: 0.2984 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8890 Z= 0.094 Angle : 0.495 6.000 12067 Z= 0.259 Chirality : 0.043 0.195 1338 Planarity : 0.004 0.050 1530 Dihedral : 5.815 48.247 1439 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 2.38 % Allowed : 16.79 % Favored : 80.83 % 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: 0.02 (0.25), residues: 1065 helix: -0.46 (0.48), residues: 122 sheet: 0.38 (0.32), residues: 242 loop : 0.05 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 650 TYR 0.014 0.001 TYR H 27 PHE 0.016 0.001 PHE H 220 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8843) covalent geometry : angle 0.48054 (11960) SS BOND : bond 0.00231 ( 34) SS BOND : angle 0.87292 ( 68) hydrogen bonds : bond 0.02830 ( 219) hydrogen bonds : angle 5.13551 ( 618) link_ALPHA1-2 : bond 0.00395 ( 2) link_ALPHA1-2 : angle 1.51141 ( 6) link_ALPHA1-3 : bond 0.01204 ( 1) link_ALPHA1-3 : angle 1.79615 ( 3) link_ALPHA1-6 : bond 0.00353 ( 1) link_ALPHA1-6 : angle 1.77087 ( 3) link_BETA1-4 : bond 0.00538 ( 4) link_BETA1-4 : angle 2.33935 ( 12) link_NAG-ASN : bond 0.00202 ( 5) link_NAG-ASN : angle 1.74652 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.281 Fit side-chains REVERT: H 25 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8763 (pt) REVERT: H 507 ASP cc_start: 0.8301 (t0) cc_final: 0.7980 (t0) REVERT: H 638 GLN cc_start: 0.7310 (pm20) cc_final: 0.6788 (pm20) REVERT: H 646 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: H 650 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7177 (ttt90) REVERT: H 701 LYS cc_start: 0.7056 (mttt) cc_final: 0.6810 (mmmm) REVERT: L 51 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.7704 (pm20) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.1157 time to fit residues: 17.0474 Evaluate side-chains 106 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 802 VAL Chi-restraints excluded: chain H residue 809 SER Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107481 restraints weight = 9277.746| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.35 r_work: 0.2945 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8890 Z= 0.119 Angle : 0.507 6.230 12067 Z= 0.264 Chirality : 0.044 0.193 1338 Planarity : 0.004 0.048 1530 Dihedral : 5.717 48.388 1439 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Rotamer: Outliers : 2.28 % Allowed : 16.58 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.00 (0.25), residues: 1065 helix: -0.50 (0.48), residues: 122 sheet: 0.37 (0.33), residues: 242 loop : 0.04 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 650 TYR 0.017 0.001 TYR H 251 PHE 0.019 0.001 PHE H 258 TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8843) covalent geometry : angle 0.49210 (11960) SS BOND : bond 0.00262 ( 34) SS BOND : angle 0.91613 ( 68) hydrogen bonds : bond 0.02919 ( 219) hydrogen bonds : angle 5.11999 ( 618) link_ALPHA1-2 : bond 0.00372 ( 2) link_ALPHA1-2 : angle 1.47277 ( 6) link_ALPHA1-3 : bond 0.00999 ( 1) link_ALPHA1-3 : angle 1.80294 ( 3) link_ALPHA1-6 : bond 0.00384 ( 1) link_ALPHA1-6 : angle 1.68629 ( 3) link_BETA1-4 : bond 0.00506 ( 4) link_BETA1-4 : angle 2.33640 ( 12) link_NAG-ASN : bond 0.00148 ( 5) link_NAG-ASN : angle 1.76800 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.354 Fit side-chains REVERT: H 25 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8751 (pt) REVERT: H 507 ASP cc_start: 0.8342 (t0) cc_final: 0.8008 (t0) REVERT: H 638 GLN cc_start: 0.7218 (pm20) cc_final: 0.6691 (pm20) REVERT: H 646 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: H 701 LYS cc_start: 0.6981 (mttt) cc_final: 0.6738 (mmmm) REVERT: L 51 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: L 94 GLU cc_start: 0.8131 (mp0) cc_final: 0.7864 (mp0) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.1198 time to fit residues: 16.4966 Evaluate side-chains 105 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 802 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.0010 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN H 232 GLN L 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.166235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109272 restraints weight = 9402.119| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.36 r_work: 0.2954 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8890 Z= 0.094 Angle : 0.486 5.942 12067 Z= 0.253 Chirality : 0.043 0.188 1338 Planarity : 0.003 0.050 1530 Dihedral : 5.314 49.065 1439 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.07 % Favored : 97.84 % Rotamer: Outliers : 2.07 % Allowed : 16.68 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.26), residues: 1065 helix: -0.36 (0.49), residues: 122 sheet: 0.40 (0.33), residues: 244 loop : 0.08 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 650 TYR 0.018 0.001 TYR H 251 PHE 0.020 0.001 PHE H 220 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8843) covalent geometry : angle 0.47286 (11960) SS BOND : bond 0.00215 ( 34) SS BOND : angle 0.81436 ( 68) hydrogen bonds : bond 0.02736 ( 219) hydrogen bonds : angle 4.95532 ( 618) link_ALPHA1-2 : bond 0.00377 ( 2) link_ALPHA1-2 : angle 1.49291 ( 6) link_ALPHA1-3 : bond 0.01155 ( 1) link_ALPHA1-3 : angle 1.58987 ( 3) link_ALPHA1-6 : bond 0.00511 ( 1) link_ALPHA1-6 : angle 1.61241 ( 3) link_BETA1-4 : bond 0.00505 ( 4) link_BETA1-4 : angle 2.14379 ( 12) link_NAG-ASN : bond 0.00167 ( 5) link_NAG-ASN : angle 1.66433 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.359 Fit side-chains REVERT: H 25 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8721 (pt) REVERT: H 224 ASP cc_start: 0.7982 (t0) cc_final: 0.7737 (t0) REVERT: H 232 GLN cc_start: 0.7200 (mt0) cc_final: 0.6989 (mt0) REVERT: H 319 MET cc_start: 0.9096 (mtp) cc_final: 0.8874 (mtm) REVERT: H 507 ASP cc_start: 0.8307 (t0) cc_final: 0.7979 (t0) REVERT: H 638 GLN cc_start: 0.7215 (pm20) cc_final: 0.6748 (pm20) REVERT: H 646 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: H 650 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7111 (ttt90) REVERT: H 701 LYS cc_start: 0.6919 (mttt) cc_final: 0.6694 (mmmm) REVERT: L 51 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.7669 (pm20) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 0.1214 time to fit residues: 16.9815 Evaluate side-chains 102 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 282 VAL Chi-restraints excluded: chain H residue 460 GLU Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 554 ASP Chi-restraints excluded: chain H residue 556 VAL Chi-restraints excluded: chain H residue 592 CYS Chi-restraints excluded: chain H residue 646 GLU Chi-restraints excluded: chain H residue 707 VAL Chi-restraints excluded: chain H residue 802 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 97 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 57 optimal weight: 0.0570 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.165899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109887 restraints weight = 9369.157| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.38 r_work: 0.2970 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8890 Z= 0.093 Angle : 0.491 5.950 12067 Z= 0.255 Chirality : 0.043 0.187 1338 Planarity : 0.004 0.058 1530 Dihedral : 5.218 49.160 1439 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.25 % Favored : 97.65 % Rotamer: Outliers : 2.38 % Allowed : 16.48 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.26), residues: 1065 helix: -0.35 (0.50), residues: 116 sheet: 0.41 (0.33), residues: 244 loop : 0.11 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 650 TYR 0.017 0.001 TYR H 251 PHE 0.019 0.001 PHE H 220 TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8843) covalent geometry : angle 0.47676 (11960) SS BOND : bond 0.00223 ( 34) SS BOND : angle 1.00004 ( 68) hydrogen bonds : bond 0.02725 ( 219) hydrogen bonds : angle 4.90717 ( 618) link_ALPHA1-2 : bond 0.00389 ( 2) link_ALPHA1-2 : angle 1.48404 ( 6) link_ALPHA1-3 : bond 0.01142 ( 1) link_ALPHA1-3 : angle 1.60066 ( 3) link_ALPHA1-6 : bond 0.00536 ( 1) link_ALPHA1-6 : angle 1.57169 ( 3) link_BETA1-4 : bond 0.00509 ( 4) link_BETA1-4 : angle 2.13953 ( 12) link_NAG-ASN : bond 0.00172 ( 5) link_NAG-ASN : angle 1.63572 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2720.63 seconds wall clock time: 47 minutes 4.88 seconds (2824.88 seconds total)