Starting phenix.real_space_refine on Fri Aug 22 20:22:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esv_28580/08_2025/8esv_28580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esv_28580/08_2025/8esv_28580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8esv_28580/08_2025/8esv_28580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esv_28580/08_2025/8esv_28580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8esv_28580/08_2025/8esv_28580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esv_28580/08_2025/8esv_28580.map" } resolution = 3.3 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= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 1 6.06 5 S 64 5.16 5 C 4568 2.51 5 N 1203 2.21 5 O 1385 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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7222 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3306 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'ARG:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2006 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 249} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 909 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 794 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 106} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' CA': 1, ' ZN': 1, 'BAT': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.24 Number of scatterers: 7222 At special positions: 0 Unit cell: (76.56, 99, 170.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 1 19.99 S 64 16.00 O 1385 8.00 N 1203 7.00 C 4568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 451 " distance=2.03 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 435 " distance=2.03 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 536 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 607 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 597 " distance=2.03 Simple disulfide: pdb=" SG CYS A 594 " - pdb=" SG CYS A 639 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 645 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 171 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 111 " 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 ALPHA1-3 " MAN C 3 " - " MAN C 4 " ALPHA1-4 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 801 " - " ASN A 551 " " NAG C 1 " - " ASN A 278 " " NAG D 1 " - " ASN A 439 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 393.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 387 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 393 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 383 " 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 37.7% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.511A pdb=" N PHE A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.620A pdb=" N THR A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.720A pdb=" N ARG A 291 " --> pdb=" O ASN A 288 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 292 " --> pdb=" O PRO A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 292' Processing helix chain 'A' and resid 296 through 307 removed outlier: 3.762A pdb=" N GLN A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 373 through 389 removed outlier: 3.749A pdb=" N ALA A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.175A pdb=" N ASN A 430 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.526A pdb=" N GLN A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 removed outlier: 4.408A pdb=" N CYS A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.622A pdb=" N LEU A 593 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 594 " --> pdb=" O LYS A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 594' Processing helix chain 'A' and resid 652 through 663 Processing helix chain 'A' and resid 664 through 670 removed outlier: 4.010A pdb=" N ILE A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 51 removed outlier: 3.757A pdb=" N LEU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP B 19 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 85 Processing helix chain 'B' and resid 88 through 116 Processing helix chain 'B' and resid 116 through 134 Processing helix chain 'B' and resid 138 through 152 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.741A pdb=" N ASP B 162 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN B 167 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B 168 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP B 170 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 removed outlier: 4.096A pdb=" N GLY B 199 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 218 through 230 Processing helix chain 'B' and resid 230 through 267 Proline residue: B 244 - end of helix Processing helix chain 'H' and resid 80 through 83 removed outlier: 3.808A pdb=" N LYS H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 80 through 83' Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.874A pdb=" N THR H 109 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 122 Processing helix chain 'L' and resid 52 through 54 No H-bonds generated for 'chain 'L' and resid 52 through 54' Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 277 removed outlier: 6.018A pdb=" N CYS A 222 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS A 273 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU A 224 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE A 275 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 226 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE A 277 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 228 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N LEU A 314 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN A 223 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N TYR A 316 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 225 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE A 318 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN A 227 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.685A pdb=" N THR A 553 " --> pdb=" O CYS A 562 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.503A pdb=" N GLU A 578 " --> pdb=" O MET A 599 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 638 through 639 Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 26 removed outlier: 3.795A pdb=" N LYS H 24 " --> pdb=" O THR H 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN H 96 " --> pdb=" O ASP H 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.933A pdb=" N VAL H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 30 through 31 removed outlier: 4.089A pdb=" N GLY H 52 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 26 through 29 removed outlier: 5.828A pdb=" N THR L 92 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N SER L 49 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N SER L 90 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 11.895A pdb=" N VAL L 51 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 12.221A pdb=" N SER L 88 " --> pdb=" O VAL L 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 32 through 35 removed outlier: 6.029A pdb=" N MET L 33 " --> pdb=" O GLU L 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 76 through 77 removed outlier: 6.510A pdb=" N TRP L 58 " --> pdb=" O TRP L 70 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR L 72 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU L 56 " --> pdb=" O TYR L 72 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN L 113 " --> pdb=" O THR L 120 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 792 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: 1.01 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1166 1.31 - 1.44: 2012 1.44 - 1.57: 4114 1.57 - 1.69: 3 1.69 - 1.82: 79 Bond restraints: 7374 Sorted by residual: bond pdb=" C5 BAT A 804 " pdb=" C6 BAT A 804 " ideal model delta sigma weight residual 1.422 1.596 -0.174 2.00e-02 2.50e+03 7.57e+01 bond pdb=" C4 BAT A 804 " pdb=" S2 BAT A 804 " ideal model delta sigma weight residual 1.726 1.554 0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C7 BAT A 804 " pdb=" S2 BAT A 804 " ideal model delta sigma weight residual 1.716 1.556 0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" C15 BAT A 804 " pdb=" N3 BAT A 804 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C2 BAT A 804 " pdb=" N1 BAT A 804 " ideal model delta sigma weight residual 1.341 1.452 -0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 9925 3.12 - 6.23: 80 6.23 - 9.35: 10 9.35 - 12.47: 1 12.47 - 15.58: 1 Bond angle restraints: 10017 Sorted by residual: angle pdb=" C4 BAT A 804 " pdb=" S2 BAT A 804 " pdb=" C7 BAT A 804 " ideal model delta sigma weight residual 92.03 107.61 -15.58 3.00e+00 1.11e-01 2.70e+01 angle pdb=" CA PRO A 374 " pdb=" N PRO A 374 " pdb=" CD PRO A 374 " ideal model delta sigma weight residual 112.00 105.31 6.69 1.40e+00 5.10e-01 2.28e+01 angle pdb=" CA PRO A 604 " pdb=" N PRO A 604 " pdb=" CD PRO A 604 " ideal model delta sigma weight residual 112.00 107.34 4.66 1.40e+00 5.10e-01 1.11e+01 angle pdb=" C GLN B 119 " pdb=" N THR B 120 " pdb=" CA THR B 120 " ideal model delta sigma weight residual 120.68 115.16 5.52 1.70e+00 3.46e-01 1.05e+01 angle pdb=" C3 BAT A 804 " pdb=" S1 BAT A 804 " pdb=" C4 BAT A 804 " ideal model delta sigma weight residual 101.64 110.02 -8.38 3.00e+00 1.11e-01 7.81e+00 ... (remaining 10012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 4052 23.30 - 46.61: 483 46.61 - 69.91: 64 69.91 - 93.21: 21 93.21 - 116.52: 12 Dihedral angle restraints: 4632 sinusoidal: 1953 harmonic: 2679 Sorted by residual: dihedral pdb=" CB CYS A 503 " pdb=" SG CYS A 503 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -166.40 80.40 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 580 " pdb=" SG CYS A 580 " pdb=" SG CYS A 607 " pdb=" CB CYS A 607 " ideal model delta sinusoidal sigma weight residual -86.00 -163.54 77.54 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 594 " pdb=" SG CYS A 594 " pdb=" SG CYS A 639 " pdb=" CB CYS A 639 " ideal model delta sinusoidal sigma weight residual 93.00 165.15 -72.15 1 1.00e+01 1.00e-02 6.66e+01 ... (remaining 4629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 923 0.051 - 0.103: 202 0.103 - 0.154: 20 0.154 - 0.206: 6 0.206 - 0.257: 4 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C14 BAT A 804 " pdb=" C15 BAT A 804 " pdb=" C17 BAT A 804 " pdb=" N2 BAT A 804 " both_signs ideal model delta sigma weight residual False 2.36 2.62 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3 MAN C 3 " pdb=" C2 MAN C 3 " pdb=" C4 MAN C 3 " pdb=" O3 MAN C 3 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.40e+00 ... (remaining 1152 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 603 " -0.098 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 604 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.081 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 373 " 0.066 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO A 374 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 374 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 374 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 87 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C ASP B 87 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP B 87 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.010 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 77 2.52 - 3.12: 5614 3.12 - 3.71: 11733 3.71 - 4.31: 15955 4.31 - 4.90: 26450 Nonbonded interactions: 59829 Sorted by model distance: nonbonded pdb="ZN ZN A 803 " pdb=" O1 BAT A 804 " model vdw 1.929 2.230 nonbonded pdb="ZN ZN A 803 " pdb=" O2 BAT A 804 " model vdw 2.059 2.230 nonbonded pdb=" O TRP H 66 " pdb=" OE1 GLN H 79 " model vdw 2.074 3.040 nonbonded pdb=" OD2 ASP A 229 " pdb=" OG1 THR A 319 " model vdw 2.279 3.040 nonbonded pdb=" O THR A 400 " pdb=" OG1 THR A 400 " model vdw 2.293 3.040 ... (remaining 59824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.006 0.174 7408 Z= 0.274 Angle : 0.720 15.582 10087 Z= 0.343 Chirality : 0.044 0.257 1155 Planarity : 0.006 0.147 1264 Dihedral : 19.205 116.516 2853 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 35.21 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.28), residues: 923 helix: 1.07 (0.32), residues: 276 sheet: -0.93 (0.47), residues: 132 loop : -1.17 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.015 0.001 TYR A 638 PHE 0.009 0.001 PHE H 46 TRP 0.015 0.001 TRP B 163 HIS 0.007 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00569 ( 7374) covalent geometry : angle 0.70770 (10017) SS BOND : bond 0.00213 ( 23) SS BOND : angle 0.97916 ( 46) hydrogen bonds : bond 0.18014 ( 288) hydrogen bonds : angle 6.99426 ( 792) metal coordination : bond 0.00798 ( 3) link_ALPHA1-3 : bond 0.00813 ( 1) link_ALPHA1-3 : angle 4.21206 ( 3) link_ALPHA1-4 : bond 0.00850 ( 2) link_ALPHA1-4 : angle 2.26491 ( 6) link_BETA1-4 : bond 0.00739 ( 2) link_BETA1-4 : angle 1.93365 ( 6) link_NAG-ASN : bond 0.00640 ( 3) link_NAG-ASN : angle 2.52051 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 TYR cc_start: 0.7511 (m-80) cc_final: 0.7087 (m-80) REVERT: A 428 ASN cc_start: 0.8643 (m110) cc_final: 0.8186 (m-40) REVERT: A 494 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8201 (ptmm) REVERT: A 599 MET cc_start: 0.6141 (pmm) cc_final: 0.5352 (pmm) REVERT: A 654 LEU cc_start: 0.8705 (mp) cc_final: 0.8450 (mm) REVERT: A 656 ARG cc_start: 0.7650 (mtm180) cc_final: 0.7421 (mtm180) REVERT: H 77 ASP cc_start: 0.8217 (t0) cc_final: 0.7964 (t0) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0738 time to fit residues: 21.6679 Evaluate side-chains 208 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 428 ASN A 457 GLN A 537 ASN A 564 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 230 ASN L 57 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122908 restraints weight = 10673.077| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.88 r_work: 0.3413 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7408 Z= 0.186 Angle : 0.653 8.350 10087 Z= 0.328 Chirality : 0.044 0.248 1155 Planarity : 0.005 0.106 1264 Dihedral : 11.928 104.647 1334 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.04 % Favored : 92.74 % Rotamer: Outliers : 4.95 % Allowed : 29.18 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.28), residues: 923 helix: 1.14 (0.31), residues: 275 sheet: -1.15 (0.45), residues: 131 loop : -1.02 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.013 0.002 TYR B 97 PHE 0.009 0.001 PHE A 552 TRP 0.011 0.001 TRP B 163 HIS 0.009 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7374) covalent geometry : angle 0.63760 (10017) SS BOND : bond 0.00367 ( 23) SS BOND : angle 1.12965 ( 46) hydrogen bonds : bond 0.04097 ( 288) hydrogen bonds : angle 5.19023 ( 792) metal coordination : bond 0.00905 ( 3) link_ALPHA1-3 : bond 0.01648 ( 1) link_ALPHA1-3 : angle 4.18351 ( 3) link_ALPHA1-4 : bond 0.01206 ( 2) link_ALPHA1-4 : angle 2.56576 ( 6) link_BETA1-4 : bond 0.00100 ( 2) link_BETA1-4 : angle 1.88208 ( 6) link_NAG-ASN : bond 0.00838 ( 3) link_NAG-ASN : angle 2.44004 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7626 (t80) cc_final: 0.7412 (t80) REVERT: A 235 TYR cc_start: 0.7885 (t80) cc_final: 0.7653 (t80) REVERT: A 431 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8196 (mtpt) REVERT: A 494 LYS cc_start: 0.8676 (ptpp) cc_final: 0.8305 (ptmm) REVERT: A 599 MET cc_start: 0.6290 (pmm) cc_final: 0.5225 (pmm) REVERT: B 96 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7627 (ttp) REVERT: B 116 PHE cc_start: 0.7872 (m-80) cc_final: 0.7392 (m-80) REVERT: B 247 LEU cc_start: 0.7790 (tt) cc_final: 0.7555 (tp) REVERT: H 57 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7894 (ptt180) outliers start: 37 outliers final: 20 residues processed: 242 average time/residue: 0.0719 time to fit residues: 23.4712 Evaluate side-chains 232 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain L residue 70 TRP Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121270 restraints weight = 10592.571| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.87 r_work: 0.3396 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7408 Z= 0.267 Angle : 0.687 5.983 10087 Z= 0.347 Chirality : 0.046 0.242 1155 Planarity : 0.005 0.088 1264 Dihedral : 10.536 98.645 1334 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 6.02 % Allowed : 27.98 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.27), residues: 923 helix: 0.87 (0.30), residues: 277 sheet: -1.38 (0.43), residues: 131 loop : -1.15 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.019 0.002 TYR B 255 PHE 0.015 0.001 PHE A 552 TRP 0.014 0.002 TRP B 163 HIS 0.013 0.002 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 7374) covalent geometry : angle 0.66651 (10017) SS BOND : bond 0.00470 ( 23) SS BOND : angle 1.47626 ( 46) hydrogen bonds : bond 0.04309 ( 288) hydrogen bonds : angle 5.02108 ( 792) metal coordination : bond 0.01369 ( 3) link_ALPHA1-3 : bond 0.01395 ( 1) link_ALPHA1-3 : angle 4.45637 ( 3) link_ALPHA1-4 : bond 0.01113 ( 2) link_ALPHA1-4 : angle 2.85317 ( 6) link_BETA1-4 : bond 0.00107 ( 2) link_BETA1-4 : angle 2.30172 ( 6) link_NAG-ASN : bond 0.01163 ( 3) link_NAG-ASN : angle 2.79105 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 494 LYS cc_start: 0.8597 (ptpp) cc_final: 0.8215 (ptmm) REVERT: A 514 GLN cc_start: 0.7900 (pm20) cc_final: 0.7700 (pm20) REVERT: B 96 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7849 (ttp) REVERT: B 201 LYS cc_start: 0.8490 (mmmm) cc_final: 0.8280 (mmmm) REVERT: B 205 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7857 (ptpp) REVERT: B 247 LEU cc_start: 0.7937 (tt) cc_final: 0.7670 (tp) REVERT: H 57 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8426 (ptt180) REVERT: H 108 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7634 (t70) REVERT: L 101 MET cc_start: 0.6634 (tmm) cc_final: 0.6136 (tmm) outliers start: 45 outliers final: 30 residues processed: 243 average time/residue: 0.0729 time to fit residues: 24.2452 Evaluate side-chains 249 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 90 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 46 optimal weight: 0.0980 chunk 64 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.2980 overall best weight: 0.1916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 HIS B 143 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124824 restraints weight = 10804.438| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.88 r_work: 0.3448 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7408 Z= 0.129 Angle : 0.626 8.796 10087 Z= 0.311 Chirality : 0.042 0.244 1155 Planarity : 0.004 0.074 1264 Dihedral : 9.806 97.081 1334 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.61 % Favored : 93.17 % Rotamer: Outliers : 4.28 % Allowed : 31.06 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.28), residues: 923 helix: 1.23 (0.31), residues: 276 sheet: -1.20 (0.43), residues: 128 loop : -1.06 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.015 0.002 TYR A 236 PHE 0.013 0.001 PHE A 552 TRP 0.011 0.001 TRP B 163 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7374) covalent geometry : angle 0.61031 (10017) SS BOND : bond 0.00291 ( 23) SS BOND : angle 1.08612 ( 46) hydrogen bonds : bond 0.03548 ( 288) hydrogen bonds : angle 4.67486 ( 792) metal coordination : bond 0.00648 ( 3) link_ALPHA1-3 : bond 0.01669 ( 1) link_ALPHA1-3 : angle 4.01242 ( 3) link_ALPHA1-4 : bond 0.01159 ( 2) link_ALPHA1-4 : angle 2.59952 ( 6) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.71179 ( 6) link_NAG-ASN : bond 0.00774 ( 3) link_NAG-ASN : angle 2.49904 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7530 (t80) cc_final: 0.7289 (t80) REVERT: A 431 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8181 (mtmt) REVERT: A 514 GLN cc_start: 0.7772 (pm20) cc_final: 0.7483 (pm20) REVERT: A 599 MET cc_start: 0.6223 (pmm) cc_final: 0.4603 (pmm) REVERT: A 656 ARG cc_start: 0.7575 (mtm180) cc_final: 0.7347 (mtm180) REVERT: B 96 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7690 (ttp) REVERT: B 119 GLN cc_start: 0.6994 (mp10) cc_final: 0.6686 (mp10) REVERT: B 122 ASP cc_start: 0.7578 (m-30) cc_final: 0.6947 (m-30) REVERT: B 205 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7782 (ptpp) REVERT: B 247 LEU cc_start: 0.7781 (tt) cc_final: 0.7503 (tp) REVERT: H 57 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8363 (ptt180) REVERT: H 132 LEU cc_start: 0.8308 (tp) cc_final: 0.7953 (tt) REVERT: L 101 MET cc_start: 0.6380 (tmm) cc_final: 0.5843 (tmm) outliers start: 32 outliers final: 21 residues processed: 238 average time/residue: 0.0775 time to fit residues: 24.4752 Evaluate side-chains 231 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 82 optimal weight: 0.0670 chunk 81 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123554 restraints weight = 10672.414| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.90 r_work: 0.3417 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7408 Z= 0.195 Angle : 0.640 7.542 10087 Z= 0.320 Chirality : 0.044 0.243 1155 Planarity : 0.005 0.069 1264 Dihedral : 9.613 95.616 1334 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.26 % Favored : 92.52 % Rotamer: Outliers : 5.09 % Allowed : 30.92 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.27), residues: 923 helix: 1.12 (0.31), residues: 276 sheet: -1.30 (0.42), residues: 131 loop : -1.09 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.014 0.002 TYR A 236 PHE 0.010 0.001 PHE A 552 TRP 0.010 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 7374) covalent geometry : angle 0.62195 (10017) SS BOND : bond 0.00374 ( 23) SS BOND : angle 1.28745 ( 46) hydrogen bonds : bond 0.03755 ( 288) hydrogen bonds : angle 4.62785 ( 792) metal coordination : bond 0.00931 ( 3) link_ALPHA1-3 : bond 0.01770 ( 1) link_ALPHA1-3 : angle 4.11434 ( 3) link_ALPHA1-4 : bond 0.01159 ( 2) link_ALPHA1-4 : angle 2.76347 ( 6) link_BETA1-4 : bond 0.00097 ( 2) link_BETA1-4 : angle 1.96540 ( 6) link_NAG-ASN : bond 0.00883 ( 3) link_NAG-ASN : angle 2.71418 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7672 (t80) cc_final: 0.7368 (t80) REVERT: A 235 TYR cc_start: 0.7949 (t80) cc_final: 0.7665 (t80) REVERT: A 254 ASP cc_start: 0.7624 (t70) cc_final: 0.7306 (t0) REVERT: A 494 LYS cc_start: 0.8638 (ptpp) cc_final: 0.8247 (ptmm) REVERT: A 514 GLN cc_start: 0.7770 (pm20) cc_final: 0.7450 (pm20) REVERT: B 119 GLN cc_start: 0.7338 (mp10) cc_final: 0.7045 (mp10) REVERT: B 205 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7618 (ptpp) REVERT: B 247 LEU cc_start: 0.7874 (tt) cc_final: 0.7588 (tp) REVERT: H 57 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8349 (ptt180) REVERT: H 132 LEU cc_start: 0.8344 (tp) cc_final: 0.7963 (tt) REVERT: L 101 MET cc_start: 0.6402 (tmm) cc_final: 0.5751 (tmm) outliers start: 38 outliers final: 26 residues processed: 237 average time/residue: 0.0794 time to fit residues: 25.0454 Evaluate side-chains 244 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 83 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 GLN B 143 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122236 restraints weight = 10670.785| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.96 r_work: 0.3410 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7408 Z= 0.201 Angle : 0.648 7.806 10087 Z= 0.326 Chirality : 0.044 0.240 1155 Planarity : 0.004 0.064 1264 Dihedral : 9.361 95.299 1334 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.48 % Favored : 92.31 % Rotamer: Outliers : 5.22 % Allowed : 31.06 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.27), residues: 923 helix: 1.11 (0.30), residues: 276 sheet: -1.31 (0.42), residues: 131 loop : -1.13 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.017 0.002 TYR A 575 PHE 0.014 0.001 PHE A 552 TRP 0.010 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 7374) covalent geometry : angle 0.62972 (10017) SS BOND : bond 0.00389 ( 23) SS BOND : angle 1.41557 ( 46) hydrogen bonds : bond 0.03725 ( 288) hydrogen bonds : angle 4.60213 ( 792) metal coordination : bond 0.00986 ( 3) link_ALPHA1-3 : bond 0.01869 ( 1) link_ALPHA1-3 : angle 3.83728 ( 3) link_ALPHA1-4 : bond 0.01095 ( 2) link_ALPHA1-4 : angle 2.68839 ( 6) link_BETA1-4 : bond 0.00089 ( 2) link_BETA1-4 : angle 1.86281 ( 6) link_NAG-ASN : bond 0.00867 ( 3) link_NAG-ASN : angle 2.67584 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7706 (t80) cc_final: 0.7350 (t80) REVERT: A 235 TYR cc_start: 0.7995 (t80) cc_final: 0.7679 (t80) REVERT: A 285 ASP cc_start: 0.7701 (t0) cc_final: 0.7466 (t0) REVERT: A 345 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 494 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8176 (ptpp) REVERT: A 514 GLN cc_start: 0.7769 (pm20) cc_final: 0.7436 (pm20) REVERT: A 599 MET cc_start: 0.6178 (pmm) cc_final: 0.4576 (pmm) REVERT: B 46 GLU cc_start: 0.7826 (tp30) cc_final: 0.7589 (tp30) REVERT: B 119 GLN cc_start: 0.7360 (mp10) cc_final: 0.6908 (mp10) REVERT: B 205 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7606 (ptpp) REVERT: B 247 LEU cc_start: 0.7894 (tt) cc_final: 0.7599 (tp) REVERT: H 108 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7251 (t70) REVERT: H 132 LEU cc_start: 0.8374 (tp) cc_final: 0.7993 (tt) REVERT: L 101 MET cc_start: 0.6401 (tmm) cc_final: 0.5652 (tmm) outliers start: 39 outliers final: 29 residues processed: 246 average time/residue: 0.0671 time to fit residues: 22.8236 Evaluate side-chains 248 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.0770 chunk 59 optimal weight: 0.4980 chunk 63 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124383 restraints weight = 10845.320| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.93 r_work: 0.3439 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7408 Z= 0.135 Angle : 0.633 10.674 10087 Z= 0.313 Chirality : 0.042 0.236 1155 Planarity : 0.004 0.061 1264 Dihedral : 8.906 95.738 1334 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.61 % Favored : 93.17 % Rotamer: Outliers : 4.42 % Allowed : 32.53 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.28), residues: 923 helix: 1.33 (0.31), residues: 276 sheet: -1.07 (0.43), residues: 128 loop : -1.12 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.017 0.002 TYR A 575 PHE 0.015 0.001 PHE A 552 TRP 0.010 0.001 TRP B 163 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7374) covalent geometry : angle 0.61831 (10017) SS BOND : bond 0.00270 ( 23) SS BOND : angle 1.22282 ( 46) hydrogen bonds : bond 0.03453 ( 288) hydrogen bonds : angle 4.44944 ( 792) metal coordination : bond 0.00618 ( 3) link_ALPHA1-3 : bond 0.01961 ( 1) link_ALPHA1-3 : angle 3.33758 ( 3) link_ALPHA1-4 : bond 0.01195 ( 2) link_ALPHA1-4 : angle 2.51436 ( 6) link_BETA1-4 : bond 0.00207 ( 2) link_BETA1-4 : angle 1.62026 ( 6) link_NAG-ASN : bond 0.00659 ( 3) link_NAG-ASN : angle 2.57181 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7618 (t80) cc_final: 0.7224 (t80) REVERT: A 235 TYR cc_start: 0.7934 (t80) cc_final: 0.7678 (t80) REVERT: A 255 THR cc_start: 0.8224 (m) cc_final: 0.7898 (p) REVERT: A 345 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 431 LYS cc_start: 0.8368 (mtmt) cc_final: 0.8084 (mtmt) REVERT: A 494 LYS cc_start: 0.8631 (ptpp) cc_final: 0.8323 (ptpp) REVERT: A 514 GLN cc_start: 0.7773 (pm20) cc_final: 0.7423 (pm20) REVERT: A 599 MET cc_start: 0.6032 (pmm) cc_final: 0.4578 (pmm) REVERT: B 53 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7603 (ttpt) REVERT: B 119 GLN cc_start: 0.7357 (mp10) cc_final: 0.6821 (mp10) REVERT: B 205 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7721 (ptpp) REVERT: B 247 LEU cc_start: 0.7783 (tt) cc_final: 0.7489 (tp) REVERT: H 108 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7239 (t70) REVERT: H 132 LEU cc_start: 0.8321 (tp) cc_final: 0.7939 (tt) REVERT: L 101 MET cc_start: 0.6307 (tmm) cc_final: 0.5484 (tmm) outliers start: 33 outliers final: 24 residues processed: 242 average time/residue: 0.0721 time to fit residues: 24.1947 Evaluate side-chains 238 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 0.4980 chunk 63 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.137900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122756 restraints weight = 10778.241| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.96 r_work: 0.3418 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7408 Z= 0.189 Angle : 0.658 8.991 10087 Z= 0.329 Chirality : 0.044 0.235 1155 Planarity : 0.004 0.061 1264 Dihedral : 8.807 96.478 1334 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.80 % Favored : 91.98 % Rotamer: Outliers : 4.55 % Allowed : 33.33 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.27), residues: 923 helix: 1.33 (0.31), residues: 270 sheet: -1.13 (0.42), residues: 131 loop : -1.10 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.016 0.002 TYR A 236 PHE 0.014 0.001 PHE A 552 TRP 0.010 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7374) covalent geometry : angle 0.64214 (10017) SS BOND : bond 0.00355 ( 23) SS BOND : angle 1.28404 ( 46) hydrogen bonds : bond 0.03666 ( 288) hydrogen bonds : angle 4.51739 ( 792) metal coordination : bond 0.00911 ( 3) link_ALPHA1-3 : bond 0.01777 ( 1) link_ALPHA1-3 : angle 3.17336 ( 3) link_ALPHA1-4 : bond 0.01138 ( 2) link_ALPHA1-4 : angle 2.62679 ( 6) link_BETA1-4 : bond 0.00091 ( 2) link_BETA1-4 : angle 1.88550 ( 6) link_NAG-ASN : bond 0.00861 ( 3) link_NAG-ASN : angle 2.74529 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.7992 (t80) cc_final: 0.7737 (t80) REVERT: A 276 ARG cc_start: 0.7813 (tpt-90) cc_final: 0.7480 (ttt90) REVERT: A 300 PHE cc_start: 0.7516 (t80) cc_final: 0.7213 (t80) REVERT: A 310 ASP cc_start: 0.7813 (m-30) cc_final: 0.7488 (m-30) REVERT: A 345 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7261 (mm-30) REVERT: A 431 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8272 (mtmt) REVERT: A 514 GLN cc_start: 0.7781 (pm20) cc_final: 0.7434 (pm20) REVERT: A 599 MET cc_start: 0.6109 (pmm) cc_final: 0.4628 (pmm) REVERT: B 53 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7605 (ttpt) REVERT: B 119 GLN cc_start: 0.7362 (mp10) cc_final: 0.6833 (mp10) REVERT: B 205 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7757 (ptpp) REVERT: B 247 LEU cc_start: 0.7863 (tt) cc_final: 0.7575 (tp) REVERT: H 108 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7287 (t70) REVERT: H 132 LEU cc_start: 0.8353 (tp) cc_final: 0.8006 (tt) REVERT: L 101 MET cc_start: 0.6335 (tmm) cc_final: 0.5480 (tmm) outliers start: 34 outliers final: 28 residues processed: 238 average time/residue: 0.0717 time to fit residues: 23.3613 Evaluate side-chains 249 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 49 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.137457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122778 restraints weight = 10716.342| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.90 r_work: 0.3417 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7408 Z= 0.208 Angle : 0.679 10.089 10087 Z= 0.342 Chirality : 0.045 0.239 1155 Planarity : 0.005 0.060 1264 Dihedral : 8.735 96.439 1334 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.13 % Favored : 91.66 % Rotamer: Outliers : 5.09 % Allowed : 32.80 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.27), residues: 923 helix: 1.19 (0.31), residues: 269 sheet: -1.11 (0.43), residues: 131 loop : -1.10 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.018 0.002 TYR A 236 PHE 0.014 0.001 PHE A 552 TRP 0.011 0.001 TRP B 163 HIS 0.009 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7374) covalent geometry : angle 0.66281 (10017) SS BOND : bond 0.00391 ( 23) SS BOND : angle 1.37406 ( 46) hydrogen bonds : bond 0.03766 ( 288) hydrogen bonds : angle 4.57773 ( 792) metal coordination : bond 0.01019 ( 3) link_ALPHA1-3 : bond 0.01388 ( 1) link_ALPHA1-3 : angle 3.23445 ( 3) link_ALPHA1-4 : bond 0.01108 ( 2) link_ALPHA1-4 : angle 2.65752 ( 6) link_BETA1-4 : bond 0.00093 ( 2) link_BETA1-4 : angle 1.93657 ( 6) link_NAG-ASN : bond 0.00913 ( 3) link_NAG-ASN : angle 2.78889 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7718 (t80) cc_final: 0.7273 (t80) REVERT: A 235 TYR cc_start: 0.7980 (t80) cc_final: 0.7710 (t80) REVERT: A 276 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (ttt90) REVERT: A 299 LYS cc_start: 0.7838 (tptp) cc_final: 0.7566 (tptp) REVERT: A 300 PHE cc_start: 0.7510 (t80) cc_final: 0.7201 (t80) REVERT: A 310 ASP cc_start: 0.7847 (m-30) cc_final: 0.7514 (m-30) REVERT: A 345 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 514 GLN cc_start: 0.7794 (pm20) cc_final: 0.7442 (pm20) REVERT: A 599 MET cc_start: 0.6128 (pmm) cc_final: 0.4642 (pmm) REVERT: B 53 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7604 (ttpt) REVERT: B 119 GLN cc_start: 0.7346 (mp10) cc_final: 0.6819 (mp10) REVERT: B 205 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7605 (ptpp) REVERT: B 247 LEU cc_start: 0.7899 (tt) cc_final: 0.7606 (tp) REVERT: H 47 SER cc_start: 0.7834 (p) cc_final: 0.7556 (t) REVERT: H 89 SER cc_start: 0.8303 (p) cc_final: 0.7936 (m) REVERT: H 108 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7314 (t70) REVERT: L 101 MET cc_start: 0.6356 (tmm) cc_final: 0.5503 (tmm) outliers start: 38 outliers final: 30 residues processed: 238 average time/residue: 0.0666 time to fit residues: 21.8761 Evaluate side-chains 241 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.136747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122227 restraints weight = 10753.267| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.85 r_work: 0.3415 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7408 Z= 0.231 Angle : 0.701 10.817 10087 Z= 0.353 Chirality : 0.046 0.246 1155 Planarity : 0.005 0.068 1264 Dihedral : 8.709 95.494 1334 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.02 % Favored : 91.77 % Rotamer: Outliers : 4.69 % Allowed : 32.80 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.27), residues: 923 helix: 0.99 (0.30), residues: 270 sheet: -1.22 (0.43), residues: 132 loop : -1.11 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.019 0.002 TYR A 236 PHE 0.018 0.001 PHE A 552 TRP 0.011 0.001 TRP B 163 HIS 0.012 0.002 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 7374) covalent geometry : angle 0.68410 (10017) SS BOND : bond 0.00413 ( 23) SS BOND : angle 1.45063 ( 46) hydrogen bonds : bond 0.03877 ( 288) hydrogen bonds : angle 4.66359 ( 792) metal coordination : bond 0.01136 ( 3) link_ALPHA1-3 : bond 0.00992 ( 1) link_ALPHA1-3 : angle 3.47692 ( 3) link_ALPHA1-4 : bond 0.01077 ( 2) link_ALPHA1-4 : angle 2.73105 ( 6) link_BETA1-4 : bond 0.00132 ( 2) link_BETA1-4 : angle 2.04430 ( 6) link_NAG-ASN : bond 0.00971 ( 3) link_NAG-ASN : angle 2.82303 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7693 (t80) cc_final: 0.7307 (t80) REVERT: A 276 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7615 (ttt180) REVERT: A 345 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 431 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8261 (mtmt) REVERT: A 514 GLN cc_start: 0.7812 (pm20) cc_final: 0.7501 (pm20) REVERT: B 53 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7451 (ttpt) REVERT: B 119 GLN cc_start: 0.7367 (mp10) cc_final: 0.6918 (mp10) REVERT: B 205 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7569 (ptpp) REVERT: B 247 LEU cc_start: 0.7760 (tt) cc_final: 0.7480 (tp) REVERT: H 47 SER cc_start: 0.7855 (p) cc_final: 0.7605 (t) REVERT: H 89 SER cc_start: 0.8327 (p) cc_final: 0.7970 (m) REVERT: H 108 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7286 (t70) REVERT: L 101 MET cc_start: 0.6430 (tmm) cc_final: 0.5555 (tmm) outliers start: 35 outliers final: 29 residues processed: 231 average time/residue: 0.0739 time to fit residues: 23.4590 Evaluate side-chains 244 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 276 ARG Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 0.0770 chunk 22 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.138060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123595 restraints weight = 10680.547| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.85 r_work: 0.3433 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7408 Z= 0.174 Angle : 0.687 10.831 10087 Z= 0.343 Chirality : 0.044 0.260 1155 Planarity : 0.005 0.067 1264 Dihedral : 8.540 94.444 1334 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.58 % Favored : 92.20 % Rotamer: Outliers : 4.42 % Allowed : 34.00 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.27), residues: 923 helix: 1.08 (0.30), residues: 272 sheet: -1.17 (0.43), residues: 131 loop : -1.12 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.029 0.002 TYR A 236 PHE 0.017 0.001 PHE A 552 TRP 0.011 0.001 TRP B 163 HIS 0.007 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 7374) covalent geometry : angle 0.67143 (10017) SS BOND : bond 0.00345 ( 23) SS BOND : angle 1.32913 ( 46) hydrogen bonds : bond 0.03694 ( 288) hydrogen bonds : angle 4.60614 ( 792) metal coordination : bond 0.00812 ( 3) link_ALPHA1-3 : bond 0.00963 ( 1) link_ALPHA1-3 : angle 3.56768 ( 3) link_ALPHA1-4 : bond 0.01159 ( 2) link_ALPHA1-4 : angle 2.67988 ( 6) link_BETA1-4 : bond 0.00127 ( 2) link_BETA1-4 : angle 1.83824 ( 6) link_NAG-ASN : bond 0.00806 ( 3) link_NAG-ASN : angle 2.75984 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.42 seconds wall clock time: 32 minutes 26.96 seconds (1946.96 seconds total)