Starting phenix.real_space_refine on Fri Jul 25 13:30:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esv_28580/07_2025/8esv_28580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esv_28580/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8esv_28580/07_2025/8esv_28580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esv_28580/07_2025/8esv_28580.map" model { file = "/net/cci-nas-00/data/ceres_data/8esv_28580/07_2025/8esv_28580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esv_28580/07_2025/8esv_28580.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} 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: {'GLN:plan1': 1, 'ASP:plan': 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, 'GLU:plan': 1, 'ARG:plan': 2, '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: 5.06, per 1000 atoms: 0.70 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: 2.18 Conformation dependent library (CDL) restraints added in 845.8 milliseconds 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: 0.86 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: 2.20 Time building geometry restraints manager: 2.53 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- 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 : 12.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.015 0.001 TRP B 163 HIS 0.007 0.001 HIS A 378 PHE 0.009 0.001 PHE H 46 TYR 0.015 0.001 TYR A 638 ARG 0.004 0.000 ARG A 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 3) link_NAG-ASN : angle 2.52051 ( 9) 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_ALPHA1-3 : bond 0.00813 ( 1) link_ALPHA1-3 : angle 4.21206 ( 3) hydrogen bonds : bond 0.18014 ( 288) hydrogen bonds : angle 6.99426 ( 792) metal coordination : bond 0.00798 ( 3) SS BOND : bond 0.00213 ( 23) SS BOND : angle 0.97916 ( 46) covalent geometry : bond 0.00569 ( 7374) covalent geometry : angle 0.70770 (10017) *********************** 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 : 0.748 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: 0.1807 time to fit residues: 52.0476 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 : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.0470 chunk 38 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 457 GLN A 537 ASN A 564 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN H 96 GLN L 57 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.123357 restraints weight = 10640.652| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.84 r_work: 0.3424 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7408 Z= 0.173 Angle : 0.644 8.272 10087 Z= 0.324 Chirality : 0.044 0.249 1155 Planarity : 0.005 0.106 1264 Dihedral : 12.190 106.240 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 : 4.69 % Allowed : 29.59 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 923 helix: 1.20 (0.31), residues: 274 sheet: -1.06 (0.45), residues: 138 loop : -1.02 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 163 HIS 0.009 0.001 HIS A 378 PHE 0.008 0.001 PHE A 552 TYR 0.012 0.002 TYR B 97 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00788 ( 3) link_NAG-ASN : angle 2.39984 ( 9) link_ALPHA1-4 : bond 0.01379 ( 2) link_ALPHA1-4 : angle 2.49577 ( 6) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 1.77671 ( 6) link_ALPHA1-3 : bond 0.01648 ( 1) link_ALPHA1-3 : angle 4.14957 ( 3) hydrogen bonds : bond 0.04192 ( 288) hydrogen bonds : angle 5.27239 ( 792) metal coordination : bond 0.00794 ( 3) SS BOND : bond 0.00412 ( 23) SS BOND : angle 1.03859 ( 46) covalent geometry : bond 0.00376 ( 7374) covalent geometry : angle 0.62958 (10017) *********************** 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 258 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7524 (t80) cc_final: 0.7322 (t80) REVERT: A 235 TYR cc_start: 0.7844 (t80) cc_final: 0.7586 (t80) REVERT: A 428 ASN cc_start: 0.8735 (m110) cc_final: 0.8477 (m-40) REVERT: A 431 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8103 (mtpt) REVERT: A 494 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8304 (ptmm) REVERT: A 599 MET cc_start: 0.6251 (pmm) cc_final: 0.5203 (pmm) REVERT: B 96 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7550 (ttp) REVERT: B 247 LEU cc_start: 0.7718 (tt) cc_final: 0.7488 (tp) REVERT: H 57 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7887 (ptt180) outliers start: 35 outliers final: 17 residues processed: 241 average time/residue: 0.1938 time to fit residues: 62.4142 Evaluate side-chains 233 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 641 VAL 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 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121978 restraints weight = 10738.299| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.85 r_work: 0.3406 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7408 Z= 0.235 Angle : 0.667 5.996 10087 Z= 0.337 Chirality : 0.045 0.250 1155 Planarity : 0.005 0.087 1264 Dihedral : 10.510 99.271 1334 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 5.35 % Allowed : 28.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 923 helix: 1.03 (0.31), residues: 276 sheet: -1.34 (0.44), residues: 131 loop : -1.15 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 163 HIS 0.010 0.002 HIS A 378 PHE 0.014 0.001 PHE A 552 TYR 0.017 0.002 TYR B 255 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd link_NAG-ASN : bond 0.01044 ( 3) link_NAG-ASN : angle 2.66495 ( 9) link_ALPHA1-4 : bond 0.01146 ( 2) link_ALPHA1-4 : angle 2.84733 ( 6) link_BETA1-4 : bond 0.00094 ( 2) link_BETA1-4 : angle 2.21877 ( 6) link_ALPHA1-3 : bond 0.01286 ( 1) link_ALPHA1-3 : angle 4.38830 ( 3) hydrogen bonds : bond 0.04178 ( 288) hydrogen bonds : angle 4.96465 ( 792) metal coordination : bond 0.01179 ( 3) SS BOND : bond 0.00440 ( 23) SS BOND : angle 1.35955 ( 46) covalent geometry : bond 0.00519 ( 7374) covalent geometry : angle 0.64795 (10017) *********************** 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 265 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6239 (mm-30) REVERT: A 494 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8233 (ptmm) REVERT: A 514 GLN cc_start: 0.7894 (pm20) cc_final: 0.7693 (pm20) REVERT: A 656 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7360 (mtm180) REVERT: B 96 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7815 (ttp) REVERT: B 205 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7803 (ptpp) REVERT: B 247 LEU cc_start: 0.7872 (tt) cc_final: 0.7605 (tp) REVERT: H 57 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8473 (ptt180) REVERT: H 108 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7577 (t70) REVERT: L 101 MET cc_start: 0.6632 (tmm) cc_final: 0.6138 (tmm) outliers start: 40 outliers final: 25 residues processed: 247 average time/residue: 0.2992 time to fit residues: 101.6410 Evaluate side-chains 245 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 398 GLU 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 73 MET 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 36 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 56 VAL 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 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN A 371 HIS ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3725 r_free = 0.3725 target = 0.136896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122371 restraints weight = 10778.534| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.86 r_work: 0.3407 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1286 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= 0.222 Angle : 0.666 8.042 10087 Z= 0.334 Chirality : 0.045 0.246 1155 Planarity : 0.005 0.075 1264 Dihedral : 10.068 97.408 1334 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.26 % Favored : 92.52 % Rotamer: Outliers : 5.35 % Allowed : 30.12 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 923 helix: 0.93 (0.30), residues: 276 sheet: -1.36 (0.43), residues: 131 loop : -1.13 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 PHE 0.012 0.001 PHE A 552 TYR 0.017 0.002 TYR A 236 ARG 0.002 0.000 ARG A 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 3) link_NAG-ASN : angle 2.72174 ( 9) link_ALPHA1-4 : bond 0.01041 ( 2) link_ALPHA1-4 : angle 2.78393 ( 6) link_BETA1-4 : bond 0.00140 ( 2) link_BETA1-4 : angle 2.06055 ( 6) link_ALPHA1-3 : bond 0.01491 ( 1) link_ALPHA1-3 : angle 4.25092 ( 3) hydrogen bonds : bond 0.03931 ( 288) hydrogen bonds : angle 4.84986 ( 792) metal coordination : bond 0.01116 ( 3) SS BOND : bond 0.00431 ( 23) SS BOND : angle 1.39437 ( 46) covalent geometry : bond 0.00488 ( 7374) covalent geometry : angle 0.64658 (10017) *********************** 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 258 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7601 (t80) cc_final: 0.7319 (t80) REVERT: A 494 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8202 (ptmm) REVERT: A 514 GLN cc_start: 0.7898 (pm20) cc_final: 0.7647 (pm20) REVERT: B 149 GLN cc_start: 0.8495 (mt0) cc_final: 0.8257 (mt0) REVERT: B 201 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8261 (mmmm) REVERT: B 205 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7839 (ptpp) REVERT: B 247 LEU cc_start: 0.7868 (tt) cc_final: 0.7581 (tp) REVERT: H 57 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8418 (ptt180) REVERT: L 101 MET cc_start: 0.6478 (tmm) cc_final: 0.5885 (tmm) outliers start: 40 outliers final: 28 residues processed: 239 average time/residue: 0.1953 time to fit residues: 62.2686 Evaluate side-chains 243 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 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 559 THR 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 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 228 MET 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 H residue 123 LEU Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 46 THR 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 2 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 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 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121159 restraints weight = 10676.926| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.89 r_work: 0.3394 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7408 Z= 0.270 Angle : 0.692 7.467 10087 Z= 0.349 Chirality : 0.046 0.238 1155 Planarity : 0.005 0.071 1264 Dihedral : 9.813 95.516 1334 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.23 % Favored : 91.55 % Rotamer: Outliers : 6.43 % Allowed : 29.45 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.27), residues: 923 helix: 0.79 (0.30), residues: 276 sheet: -1.42 (0.43), residues: 131 loop : -1.18 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 163 HIS 0.012 0.002 HIS A 378 PHE 0.017 0.001 PHE A 552 TYR 0.017 0.002 TYR B 97 ARG 0.002 0.000 ARG A 493 Details of bonding type rmsd link_NAG-ASN : bond 0.01228 ( 3) link_NAG-ASN : angle 3.01404 ( 9) link_ALPHA1-4 : bond 0.01113 ( 2) link_ALPHA1-4 : angle 2.95767 ( 6) link_BETA1-4 : bond 0.00102 ( 2) link_BETA1-4 : angle 2.21569 ( 6) link_ALPHA1-3 : bond 0.01761 ( 1) link_ALPHA1-3 : angle 4.22213 ( 3) hydrogen bonds : bond 0.04094 ( 288) hydrogen bonds : angle 4.88742 ( 792) metal coordination : bond 0.01241 ( 3) SS BOND : bond 0.00520 ( 23) SS BOND : angle 1.53479 ( 46) covalent geometry : bond 0.00592 ( 7374) covalent geometry : angle 0.67077 (10017) *********************** 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 266 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7705 (t80) cc_final: 0.7273 (t80) REVERT: A 514 GLN cc_start: 0.7889 (pm20) cc_final: 0.7606 (pm20) REVERT: A 656 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7365 (mtm180) REVERT: B 46 GLU cc_start: 0.7840 (tp30) cc_final: 0.7609 (tp30) REVERT: B 47 VAL cc_start: 0.7760 (t) cc_final: 0.7494 (p) REVERT: B 104 ILE cc_start: 0.8226 (tp) cc_final: 0.7908 (tp) REVERT: B 112 VAL cc_start: 0.8783 (p) cc_final: 0.8561 (p) REVERT: B 149 GLN cc_start: 0.8392 (mt0) cc_final: 0.8188 (mt0) REVERT: B 205 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7821 (ptpp) REVERT: B 247 LEU cc_start: 0.7914 (tt) cc_final: 0.7633 (tp) REVERT: H 57 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8334 (ptt180) REVERT: L 101 MET cc_start: 0.6429 (tmm) cc_final: 0.5701 (tmm) outliers start: 48 outliers final: 35 residues processed: 245 average time/residue: 0.1865 time to fit residues: 61.8876 Evaluate side-chains 252 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 324 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 379 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 559 THR 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 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 57 ARG Chi-restraints excluded: chain H residue 82 LEU 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 46 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.5980 chunk 63 optimal weight: 0.0770 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 69 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3744 r_free = 0.3744 target = 0.138237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123815 restraints weight = 10645.299| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.86 r_work: 0.3434 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7408 Z= 0.150 Angle : 0.639 7.511 10087 Z= 0.320 Chirality : 0.043 0.240 1155 Planarity : 0.005 0.063 1264 Dihedral : 9.316 95.740 1334 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 5.22 % Allowed : 32.13 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 923 helix: 1.09 (0.31), residues: 275 sheet: -1.37 (0.41), residues: 131 loop : -1.12 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 163 HIS 0.006 0.001 HIS A 378 PHE 0.015 0.001 PHE A 552 TYR 0.017 0.002 TYR A 236 ARG 0.007 0.000 ARG A 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00779 ( 3) link_NAG-ASN : angle 2.71181 ( 9) link_ALPHA1-4 : bond 0.01117 ( 2) link_ALPHA1-4 : angle 2.61947 ( 6) link_BETA1-4 : bond 0.00172 ( 2) link_BETA1-4 : angle 1.74377 ( 6) link_ALPHA1-3 : bond 0.01875 ( 1) link_ALPHA1-3 : angle 3.68021 ( 3) hydrogen bonds : bond 0.03623 ( 288) hydrogen bonds : angle 4.68569 ( 792) metal coordination : bond 0.00670 ( 3) SS BOND : bond 0.00322 ( 23) SS BOND : angle 1.12551 ( 46) covalent geometry : bond 0.00330 ( 7374) covalent geometry : angle 0.62392 (10017) *********************** 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 264 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.750 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: 0.7220 (t80) REVERT: A 234 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7869 (ttpt) REVERT: A 345 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 514 GLN cc_start: 0.7756 (pm20) cc_final: 0.7450 (pm20) REVERT: A 656 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7305 (mtm180) REVERT: B 53 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7481 (ttpt) REVERT: B 122 ASP cc_start: 0.7565 (m-30) cc_final: 0.6932 (m-30) REVERT: B 149 GLN cc_start: 0.8477 (mt0) cc_final: 0.8195 (mt0) REVERT: B 205 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7774 (ptpp) REVERT: B 247 LEU cc_start: 0.7754 (tt) cc_final: 0.7455 (tp) REVERT: H 132 LEU cc_start: 0.8332 (tp) cc_final: 0.7943 (tt) REVERT: L 101 MET cc_start: 0.6388 (tmm) cc_final: 0.5630 (tmm) outliers start: 39 outliers final: 28 residues processed: 248 average time/residue: 0.1812 time to fit residues: 60.6585 Evaluate side-chains 247 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 53 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 MET 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 B residue 228 MET 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 82 LEU 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 32 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 chunk 15 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123516 restraints weight = 10612.777| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.90 r_work: 0.3425 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7408 Z= 0.167 Angle : 0.655 10.924 10087 Z= 0.326 Chirality : 0.043 0.239 1155 Planarity : 0.004 0.061 1264 Dihedral : 9.050 95.840 1334 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.48 % Favored : 92.31 % Rotamer: Outliers : 5.49 % Allowed : 31.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 923 helix: 1.06 (0.30), residues: 275 sheet: -1.24 (0.42), residues: 131 loop : -1.15 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 163 HIS 0.009 0.001 HIS A 378 PHE 0.019 0.001 PHE B 123 TYR 0.019 0.002 TYR A 575 ARG 0.008 0.000 ARG A 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00770 ( 3) link_NAG-ASN : angle 2.70329 ( 9) link_ALPHA1-4 : bond 0.01172 ( 2) link_ALPHA1-4 : angle 2.63326 ( 6) link_BETA1-4 : bond 0.00130 ( 2) link_BETA1-4 : angle 1.80447 ( 6) link_ALPHA1-3 : bond 0.01914 ( 1) link_ALPHA1-3 : angle 3.40446 ( 3) hydrogen bonds : bond 0.03632 ( 288) hydrogen bonds : angle 4.59874 ( 792) metal coordination : bond 0.00695 ( 3) SS BOND : bond 0.00353 ( 23) SS BOND : angle 1.39574 ( 46) covalent geometry : bond 0.00370 ( 7374) covalent geometry : angle 0.63808 (10017) *********************** 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 261 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 220 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7715 (t80) cc_final: 0.7239 (t80) REVERT: A 234 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7869 (ttpt) REVERT: A 235 TYR cc_start: 0.7960 (t80) cc_final: 0.7652 (t80) REVERT: A 345 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7151 (mm-30) REVERT: A 431 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8266 (mtmt) REVERT: A 514 GLN cc_start: 0.7773 (pm20) cc_final: 0.7436 (pm20) REVERT: A 599 MET cc_start: 0.6143 (pmm) cc_final: 0.4590 (pmm) REVERT: B 46 GLU cc_start: 0.7826 (tp30) cc_final: 0.7574 (tp30) REVERT: B 53 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7490 (ttpt) REVERT: B 205 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7630 (ptpp) REVERT: B 247 LEU cc_start: 0.7853 (tt) cc_final: 0.7565 (tp) REVERT: H 132 LEU cc_start: 0.8320 (tp) cc_final: 0.7927 (tt) REVERT: L 101 MET cc_start: 0.6354 (tmm) cc_final: 0.5582 (tmm) outliers start: 41 outliers final: 31 residues processed: 243 average time/residue: 0.1919 time to fit residues: 61.6672 Evaluate side-chains 253 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 411 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 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 641 VAL Chi-restraints excluded: chain B residue 37 LEU 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 82 LEU 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 Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 73 optimal weight: 0.0270 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122967 restraints weight = 10842.056| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.91 r_work: 0.3421 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1565 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= 0.193 Angle : 0.663 9.053 10087 Z= 0.334 Chirality : 0.044 0.237 1155 Planarity : 0.005 0.060 1264 Dihedral : 8.907 97.183 1334 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.80 % Favored : 91.98 % Rotamer: Outliers : 4.55 % Allowed : 33.60 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 923 helix: 1.02 (0.30), residues: 276 sheet: -1.24 (0.42), residues: 131 loop : -1.16 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 163 HIS 0.009 0.001 HIS A 378 PHE 0.022 0.001 PHE B 123 TYR 0.019 0.002 TYR A 575 ARG 0.005 0.000 ARG A 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 3) link_NAG-ASN : angle 2.77021 ( 9) link_ALPHA1-4 : bond 0.01150 ( 2) link_ALPHA1-4 : angle 2.63705 ( 6) link_BETA1-4 : bond 0.00102 ( 2) link_BETA1-4 : angle 1.88789 ( 6) link_ALPHA1-3 : bond 0.01661 ( 1) link_ALPHA1-3 : angle 3.20553 ( 3) hydrogen bonds : bond 0.03694 ( 288) hydrogen bonds : angle 4.61171 ( 792) metal coordination : bond 0.00928 ( 3) SS BOND : bond 0.00379 ( 23) SS BOND : angle 1.38909 ( 46) covalent geometry : bond 0.00427 ( 7374) covalent geometry : angle 0.64648 (10017) *********************** 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 254 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7712 (t80) cc_final: 0.7183 (t80) REVERT: A 235 TYR cc_start: 0.7999 (t80) cc_final: 0.7644 (t80) REVERT: A 276 ARG cc_start: 0.7828 (tpt-90) cc_final: 0.7589 (ttt180) REVERT: A 299 LYS cc_start: 0.7818 (tptp) cc_final: 0.7607 (tptp) REVERT: A 345 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 431 LYS cc_start: 0.8501 (mtmt) cc_final: 0.8259 (mtmt) REVERT: A 514 GLN cc_start: 0.7791 (pm20) cc_final: 0.7455 (pm20) REVERT: A 599 MET cc_start: 0.6110 (pmm) cc_final: 0.4548 (pmm) REVERT: B 46 GLU cc_start: 0.7807 (tp30) cc_final: 0.7570 (tp30) REVERT: B 47 VAL cc_start: 0.7812 (t) cc_final: 0.7545 (p) REVERT: B 53 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7489 (ttpt) REVERT: B 205 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7775 (ptpp) REVERT: B 247 LEU cc_start: 0.7804 (tt) cc_final: 0.7502 (tp) REVERT: H 132 LEU cc_start: 0.8353 (tp) cc_final: 0.7973 (tt) REVERT: L 101 MET cc_start: 0.6405 (tmm) cc_final: 0.5574 (tmm) outliers start: 34 outliers final: 29 residues processed: 242 average time/residue: 0.2073 time to fit residues: 67.4417 Evaluate side-chains 245 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 504 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 54 THR 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 82 LEU 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 81 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121199 restraints weight = 10731.766| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.84 r_work: 0.3398 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7408 Z= 0.280 Angle : 0.727 9.521 10087 Z= 0.367 Chirality : 0.047 0.235 1155 Planarity : 0.005 0.060 1264 Dihedral : 8.943 95.806 1334 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.67 % Favored : 91.12 % Rotamer: Outliers : 5.35 % Allowed : 32.93 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.27), residues: 923 helix: 0.77 (0.30), residues: 271 sheet: -1.28 (0.43), residues: 132 loop : -1.19 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 615 HIS 0.014 0.002 HIS A 378 PHE 0.027 0.002 PHE B 123 TYR 0.018 0.002 TYR H 113 ARG 0.003 0.000 ARG A 438 Details of bonding type rmsd link_NAG-ASN : bond 0.01215 ( 3) link_NAG-ASN : angle 2.91491 ( 9) link_ALPHA1-4 : bond 0.01050 ( 2) link_ALPHA1-4 : angle 2.88374 ( 6) link_BETA1-4 : bond 0.00226 ( 2) link_BETA1-4 : angle 2.26742 ( 6) link_ALPHA1-3 : bond 0.01127 ( 1) link_ALPHA1-3 : angle 3.39328 ( 3) hydrogen bonds : bond 0.04101 ( 288) hydrogen bonds : angle 4.83078 ( 792) metal coordination : bond 0.01334 ( 3) SS BOND : bond 0.00494 ( 23) SS BOND : angle 1.60182 ( 46) covalent geometry : bond 0.00618 ( 7374) covalent geometry : angle 0.70757 (10017) *********************** 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 250 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7851 (t80) cc_final: 0.7283 (t80) REVERT: A 235 TYR cc_start: 0.8112 (t80) cc_final: 0.7864 (t80) REVERT: A 299 LYS cc_start: 0.7883 (tptp) cc_final: 0.7654 (tptp) REVERT: A 345 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 514 GLN cc_start: 0.7794 (pm20) cc_final: 0.7486 (pm20) REVERT: A 564 ASN cc_start: 0.7949 (m-40) cc_final: 0.7710 (m-40) REVERT: B 47 VAL cc_start: 0.7805 (t) cc_final: 0.7573 (p) REVERT: B 53 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7527 (ttpt) REVERT: B 112 VAL cc_start: 0.8753 (p) cc_final: 0.8497 (p) REVERT: B 205 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7824 (ptpp) REVERT: B 247 LEU cc_start: 0.7910 (tt) cc_final: 0.7613 (tp) REVERT: H 47 SER cc_start: 0.7806 (p) cc_final: 0.7528 (t) REVERT: H 89 SER cc_start: 0.8344 (p) cc_final: 0.8052 (t) REVERT: L 101 MET cc_start: 0.6419 (tmm) cc_final: 0.5552 (tmm) outliers start: 40 outliers final: 32 residues processed: 235 average time/residue: 0.2663 time to fit residues: 85.2011 Evaluate side-chains 246 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER 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 504 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 25 ILE 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 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 B residue 241 ILE 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 82 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 0.0370 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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** A 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123325 restraints weight = 10770.859| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.84 r_work: 0.3413 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1723 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= 0.214 Angle : 0.707 11.583 10087 Z= 0.354 Chirality : 0.046 0.249 1155 Planarity : 0.005 0.069 1264 Dihedral : 8.760 95.020 1334 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.48 % Favored : 92.31 % Rotamer: Outliers : 4.69 % Allowed : 33.87 % Favored : 61.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.27), residues: 923 helix: 0.70 (0.30), residues: 276 sheet: -1.30 (0.42), residues: 131 loop : -1.18 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 163 HIS 0.010 0.002 HIS A 378 PHE 0.023 0.001 PHE B 123 TYR 0.026 0.002 TYR A 236 ARG 0.004 0.000 ARG A 557 Details of bonding type rmsd link_NAG-ASN : bond 0.00917 ( 3) link_NAG-ASN : angle 2.87405 ( 9) link_ALPHA1-4 : bond 0.01105 ( 2) link_ALPHA1-4 : angle 2.74992 ( 6) link_BETA1-4 : bond 0.00143 ( 2) link_BETA1-4 : angle 1.99851 ( 6) link_ALPHA1-3 : bond 0.01000 ( 1) link_ALPHA1-3 : angle 3.51508 ( 3) hydrogen bonds : bond 0.03856 ( 288) hydrogen bonds : angle 4.78120 ( 792) metal coordination : bond 0.01026 ( 3) SS BOND : bond 0.00409 ( 23) SS BOND : angle 1.51610 ( 46) covalent geometry : bond 0.00473 ( 7374) covalent geometry : angle 0.68869 (10017) ********************** 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 245 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 210 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7821 (t80) cc_final: 0.7225 (t80) REVERT: A 235 TYR cc_start: 0.8019 (t80) cc_final: 0.7776 (t80) REVERT: A 299 LYS cc_start: 0.7911 (tptp) cc_final: 0.7670 (tptp) REVERT: A 345 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 420 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7415 (mtp85) REVERT: A 494 LYS cc_start: 0.8544 (ptpp) cc_final: 0.8230 (ptmm) REVERT: A 514 GLN cc_start: 0.7801 (pm20) cc_final: 0.7481 (pm20) REVERT: A 564 ASN cc_start: 0.7903 (m-40) cc_final: 0.7647 (m-40) REVERT: A 599 MET cc_start: 0.6186 (pmm) cc_final: 0.4641 (pmm) REVERT: B 47 VAL cc_start: 0.7627 (t) cc_final: 0.7419 (p) REVERT: B 53 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7453 (ttpt) REVERT: B 122 ASP cc_start: 0.7660 (m-30) cc_final: 0.7241 (m-30) REVERT: B 205 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7751 (ptpp) REVERT: B 247 LEU cc_start: 0.7765 (tt) cc_final: 0.7478 (tp) REVERT: H 47 SER cc_start: 0.7839 (p) cc_final: 0.7583 (t) REVERT: H 89 SER cc_start: 0.8356 (p) cc_final: 0.8071 (t) REVERT: L 101 MET cc_start: 0.6463 (tmm) cc_final: 0.5555 (tmm) outliers start: 35 outliers final: 31 residues processed: 233 average time/residue: 0.2962 time to fit residues: 91.2231 Evaluate side-chains 238 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER 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 504 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER 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 82 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123923 restraints weight = 10658.176| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.86 r_work: 0.3434 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1715 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= 0.160 Angle : 0.681 11.167 10087 Z= 0.341 Chirality : 0.044 0.279 1155 Planarity : 0.005 0.067 1264 Dihedral : 8.570 94.798 1334 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.58 % Favored : 92.20 % Rotamer: Outliers : 4.28 % Allowed : 33.87 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.27), residues: 923 helix: 0.91 (0.30), residues: 275 sheet: -1.29 (0.43), residues: 131 loop : -1.12 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 163 HIS 0.006 0.001 HIS A 595 PHE 0.021 0.001 PHE B 123 TYR 0.023 0.002 TYR A 236 ARG 0.003 0.000 ARG A 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00743 ( 3) link_NAG-ASN : angle 2.75178 ( 9) link_ALPHA1-4 : bond 0.01187 ( 2) link_ALPHA1-4 : angle 2.63613 ( 6) link_BETA1-4 : bond 0.00130 ( 2) link_BETA1-4 : angle 1.77109 ( 6) link_ALPHA1-3 : bond 0.00987 ( 1) link_ALPHA1-3 : angle 3.58351 ( 3) hydrogen bonds : bond 0.03632 ( 288) hydrogen bonds : angle 4.65868 ( 792) metal coordination : bond 0.00736 ( 3) SS BOND : bond 0.00337 ( 23) SS BOND : angle 1.32213 ( 46) covalent geometry : bond 0.00353 ( 7374) covalent geometry : angle 0.66511 (10017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.61 seconds wall clock time: 82 minutes 34.71 seconds (4954.71 seconds total)