Starting phenix.real_space_refine on Tue Sep 24 09:15:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esv_28580/09_2024/8esv_28580.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esv_28580/09_2024/8esv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esv_28580/09_2024/8esv_28580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esv_28580/09_2024/8esv_28580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esv_28580/09_2024/8esv_28580.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8esv_28580/09_2024/8esv_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-5461/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: 5.23, per 1000 atoms: 0.72 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: 2.86 Conformation dependent library (CDL) restraints added in 924.7 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: 0.88 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: 2.29 Time building geometry restraints manager: 2.69 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.530 Find NCS groups from input model: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- 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 7374 Z= 0.329 Angle : 0.708 15.582 10017 Z= 0.340 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.809 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: 0.1778 time to fit residues: 51.0845 Evaluate side-chains 208 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 428 ASN A 457 GLN A 537 ASN A 564 ASN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 230 ASN H 96 GLN L 57 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7374 Z= 0.291 Angle : 0.647 8.357 10017 Z= 0.330 Chirality : 0.045 0.247 1155 Planarity : 0.005 0.106 1264 Dihedral : 12.025 104.618 1334 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.04 % Favored : 92.74 % Rotamer: Outliers : 4.82 % Allowed : 29.18 % 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: -0.62 (0.28), residues: 923 helix: 1.10 (0.31), residues: 275 sheet: -1.17 (0.45), residues: 131 loop : -1.04 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 PHE 0.009 0.001 PHE A 552 TYR 0.013 0.002 TYR A 316 ARG 0.003 0.001 ARG A 420 *********************** 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 257 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8053 (mtpt) REVERT: A 494 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8249 (ptmm) REVERT: A 514 GLN cc_start: 0.7705 (pm20) cc_final: 0.7503 (pm20) REVERT: A 599 MET cc_start: 0.6281 (pmm) cc_final: 0.5196 (pmm) REVERT: B 96 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7770 (ttp) REVERT: B 116 PHE cc_start: 0.7830 (m-80) cc_final: 0.7350 (m-80) REVERT: B 247 LEU cc_start: 0.7932 (tt) cc_final: 0.7705 (tp) REVERT: H 57 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7874 (ptt180) outliers start: 36 outliers final: 19 residues processed: 239 average time/residue: 0.1880 time to fit residues: 59.7380 Evaluate side-chains 230 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 209 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 73 MET 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 46 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7374 Z= 0.345 Angle : 0.651 5.894 10017 Z= 0.334 Chirality : 0.045 0.243 1155 Planarity : 0.005 0.087 1264 Dihedral : 10.515 99.216 1334 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.58 % Favored : 92.20 % Rotamer: Outliers : 5.89 % Allowed : 28.25 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.27), residues: 923 helix: 0.96 (0.30), residues: 276 sheet: -1.34 (0.43), residues: 131 loop : -1.14 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 163 HIS 0.011 0.002 HIS A 378 PHE 0.014 0.001 PHE A 552 TYR 0.013 0.002 TYR B 97 ARG 0.002 0.000 ARG A 493 *********************** 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 266 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7584 (t80) cc_final: 0.7287 (t80) REVERT: A 400 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8265 (p) REVERT: A 494 LYS cc_start: 0.8544 (ptpp) cc_final: 0.8189 (ptmm) REVERT: A 514 GLN cc_start: 0.7693 (pm20) cc_final: 0.7438 (pm20) REVERT: B 96 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (ttp) REVERT: B 205 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7820 (ptpp) REVERT: B 247 LEU cc_start: 0.7975 (tt) cc_final: 0.7719 (tp) REVERT: H 108 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7628 (t70) REVERT: L 101 MET cc_start: 0.6896 (tmm) cc_final: 0.6496 (tmm) outliers start: 44 outliers final: 30 residues processed: 245 average time/residue: 0.1864 time to fit residues: 61.3526 Evaluate side-chains 249 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 400 THR 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 132 ILE 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 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 56 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.0670 chunk 62 optimal weight: 0.0270 chunk 43 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.0050 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.2390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7374 Z= 0.198 Angle : 0.612 8.766 10017 Z= 0.309 Chirality : 0.042 0.244 1155 Planarity : 0.004 0.074 1264 Dihedral : 9.914 97.514 1334 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.61 % Favored : 93.17 % Rotamer: Outliers : 5.09 % Allowed : 29.72 % Favored : 65.19 % 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: -0.60 (0.28), residues: 923 helix: 1.21 (0.31), residues: 276 sheet: -1.20 (0.43), residues: 128 loop : -1.09 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 163 HIS 0.006 0.001 HIS A 378 PHE 0.014 0.001 PHE A 552 TYR 0.015 0.002 TYR A 236 ARG 0.002 0.000 ARG B 129 *********************** 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 256 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7566 (t80) cc_final: 0.7201 (t80) REVERT: A 400 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 431 LYS cc_start: 0.8376 (mtmt) cc_final: 0.8063 (mtmt) REVERT: A 514 GLN cc_start: 0.7577 (pm20) cc_final: 0.7280 (pm20) REVERT: A 599 MET cc_start: 0.6242 (pmm) cc_final: 0.4592 (pmm) REVERT: A 656 ARG cc_start: 0.7643 (mtm180) cc_final: 0.7372 (mtm180) REVERT: B 96 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7754 (ttp) REVERT: B 205 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7790 (ptpp) REVERT: B 247 LEU cc_start: 0.7842 (tt) cc_final: 0.7551 (tp) REVERT: L 101 MET cc_start: 0.6690 (tmm) cc_final: 0.6244 (tmm) outliers start: 38 outliers final: 24 residues processed: 241 average time/residue: 0.2089 time to fit residues: 66.7099 Evaluate side-chains 234 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 7374 Z= 0.447 Angle : 0.690 7.283 10017 Z= 0.354 Chirality : 0.047 0.246 1155 Planarity : 0.005 0.072 1264 Dihedral : 9.938 95.938 1334 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.13 % Favored : 91.66 % Rotamer: Outliers : 5.76 % Allowed : 30.25 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.27), residues: 923 helix: 0.74 (0.30), residues: 277 sheet: -1.46 (0.42), residues: 132 loop : -1.20 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 66 HIS 0.013 0.002 HIS A 378 PHE 0.014 0.002 PHE H 46 TYR 0.016 0.002 TYR H 113 ARG 0.003 0.000 ARG A 557 *********************** 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 262 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 470 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6101 (mm-30) REVERT: A 494 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8279 (ptpp) REVERT: A 514 GLN cc_start: 0.7710 (pm20) cc_final: 0.7412 (pm20) REVERT: B 47 VAL cc_start: 0.7854 (t) cc_final: 0.7593 (p) REVERT: B 96 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7875 (ttp) REVERT: B 104 ILE cc_start: 0.8170 (tp) cc_final: 0.7852 (tp) REVERT: B 205 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7796 (ptpp) REVERT: B 247 LEU cc_start: 0.7994 (tt) cc_final: 0.7712 (tp) REVERT: H 132 LEU cc_start: 0.8520 (tp) cc_final: 0.8110 (tt) REVERT: L 101 MET cc_start: 0.6719 (tmm) cc_final: 0.6153 (tmm) outliers start: 43 outliers final: 33 residues processed: 241 average time/residue: 0.1891 time to fit residues: 60.4889 Evaluate side-chains 256 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 400 THR 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 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 132 ILE Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 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 Chi-restraints excluded: chain L residue 120 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 85 optimal weight: 0.9990 overall best weight: 0.2918 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7374 Z= 0.220 Angle : 0.624 7.572 10017 Z= 0.316 Chirality : 0.043 0.241 1155 Planarity : 0.004 0.064 1264 Dihedral : 9.382 95.523 1334 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 4.82 % Allowed : 32.53 % 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: -0.75 (0.27), residues: 923 helix: 1.01 (0.31), residues: 275 sheet: -1.32 (0.41), residues: 131 loop : -1.11 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 163 HIS 0.007 0.001 HIS A 378 PHE 0.011 0.001 PHE A 552 TYR 0.016 0.002 TYR A 236 ARG 0.002 0.000 ARG B 129 *********************** 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 246 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 THR cc_start: 0.8461 (m) cc_final: 0.8145 (p) REVERT: A 345 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 400 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8213 (p) REVERT: A 494 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8179 (ptpp) REVERT: A 514 GLN cc_start: 0.7595 (pm20) cc_final: 0.7273 (pm20) REVERT: B 53 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7511 (ttpt) REVERT: B 96 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7743 (ttp) REVERT: B 205 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7803 (ptpp) REVERT: B 247 LEU cc_start: 0.7834 (tt) cc_final: 0.7550 (tp) REVERT: H 132 LEU cc_start: 0.8379 (tp) cc_final: 0.8003 (tt) REVERT: L 101 MET cc_start: 0.6662 (tmm) cc_final: 0.6062 (tmm) outliers start: 36 outliers final: 27 residues processed: 231 average time/residue: 0.1814 time to fit residues: 56.4945 Evaluate side-chains 235 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 204 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 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 96 MET 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 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 82 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 51 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 10 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 40 optimal weight: 0.0570 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7374 Z= 0.291 Angle : 0.652 10.246 10017 Z= 0.330 Chirality : 0.045 0.240 1155 Planarity : 0.005 0.063 1264 Dihedral : 9.211 95.315 1334 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.58 % Favored : 92.20 % Rotamer: Outliers : 4.82 % Allowed : 32.40 % Favored : 62.78 % 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: -0.79 (0.27), residues: 923 helix: 0.98 (0.30), residues: 275 sheet: -1.32 (0.41), residues: 131 loop : -1.15 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 PHE 0.012 0.001 PHE H 46 TYR 0.021 0.002 TYR A 575 ARG 0.010 0.001 ARG A 276 *********************** 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 248 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8071 (t80) cc_final: 0.7817 (t80) REVERT: A 345 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 400 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 514 GLN cc_start: 0.7598 (pm20) cc_final: 0.7276 (pm20) REVERT: A 599 MET cc_start: 0.6174 (pmm) cc_final: 0.4616 (pmm) REVERT: B 53 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7535 (ttpt) REVERT: B 205 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7727 (ptpp) REVERT: B 247 LEU cc_start: 0.7889 (tt) cc_final: 0.7604 (tp) REVERT: H 132 LEU cc_start: 0.8399 (tp) cc_final: 0.8024 (tt) REVERT: L 101 MET cc_start: 0.6642 (tmm) cc_final: 0.6011 (tmm) outliers start: 36 outliers final: 28 residues processed: 233 average time/residue: 0.1765 time to fit residues: 56.4067 Evaluate side-chains 249 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 400 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 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 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 69 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.0000 overall best weight: 0.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7374 Z= 0.247 Angle : 0.646 9.363 10017 Z= 0.326 Chirality : 0.043 0.237 1155 Planarity : 0.004 0.060 1264 Dihedral : 8.925 97.236 1334 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.85 % Rotamer: Outliers : 4.42 % Allowed : 32.80 % Favored : 62.78 % 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 (0.31), residues: 275 sheet: -1.27 (0.42), residues: 131 loop : -1.13 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 163 HIS 0.008 0.001 HIS A 378 PHE 0.017 0.001 PHE A 552 TYR 0.017 0.002 TYR A 575 ARG 0.004 0.000 ARG A 420 *********************** 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 240 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8058 (t80) cc_final: 0.7772 (t80) REVERT: A 285 ASP cc_start: 0.6805 (t0) cc_final: 0.6550 (t70) REVERT: A 299 LYS cc_start: 0.7700 (tptp) cc_final: 0.7406 (tptp) REVERT: A 345 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 400 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8227 (p) REVERT: A 431 LYS cc_start: 0.8377 (mtmt) cc_final: 0.8141 (mtmt) REVERT: A 514 GLN cc_start: 0.7602 (pm20) cc_final: 0.7271 (pm20) REVERT: A 599 MET cc_start: 0.6081 (pmm) cc_final: 0.4591 (pmm) REVERT: B 53 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7514 (ttpt) REVERT: B 205 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7738 (ptpp) REVERT: B 247 LEU cc_start: 0.7849 (tt) cc_final: 0.7559 (tp) REVERT: H 47 SER cc_start: 0.7947 (p) cc_final: 0.7637 (t) REVERT: H 89 SER cc_start: 0.8284 (p) cc_final: 0.7923 (m) REVERT: L 101 MET cc_start: 0.6628 (tmm) cc_final: 0.5922 (tmm) REVERT: L 113 GLN cc_start: 0.8056 (pp30) cc_final: 0.7851 (pp30) outliers start: 33 outliers final: 25 residues processed: 228 average time/residue: 0.1784 time to fit residues: 55.1343 Evaluate side-chains 230 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 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 400 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 524 CYS Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 559 THR Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain H residue 34 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain L residue 112 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.0370 chunk 54 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7374 Z= 0.221 Angle : 0.631 9.165 10017 Z= 0.321 Chirality : 0.043 0.239 1155 Planarity : 0.004 0.065 1264 Dihedral : 8.724 97.220 1334 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.37 % Favored : 92.42 % Rotamer: Outliers : 4.69 % Allowed : 32.40 % Favored : 62.92 % 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: -0.59 (0.28), residues: 923 helix: 1.24 (0.31), residues: 269 sheet: -1.17 (0.42), residues: 131 loop : -1.06 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 163 HIS 0.007 0.001 HIS A 378 PHE 0.015 0.001 PHE A 552 TYR 0.017 0.002 TYR A 236 ARG 0.008 0.000 ARG A 276 *********************** 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 244 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TYR cc_start: 0.7566 (m-80) cc_final: 0.7137 (m-80) REVERT: A 345 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 400 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 431 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8096 (mtmt) REVERT: A 514 GLN cc_start: 0.7601 (pm20) cc_final: 0.7026 (pm20) REVERT: A 599 MET cc_start: 0.6014 (pmm) cc_final: 0.4571 (pmm) REVERT: B 53 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7494 (ttpt) REVERT: B 205 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7816 (ptpp) REVERT: B 247 LEU cc_start: 0.7880 (tt) cc_final: 0.7597 (tp) REVERT: H 47 SER cc_start: 0.7977 (p) cc_final: 0.7655 (t) REVERT: H 89 SER cc_start: 0.8325 (p) cc_final: 0.7952 (m) REVERT: L 101 MET cc_start: 0.6614 (tmm) cc_final: 0.5909 (tmm) outliers start: 35 outliers final: 27 residues processed: 234 average time/residue: 0.1768 time to fit residues: 56.2558 Evaluate side-chains 230 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 400 THR 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 504 SER 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 107 LEU 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 37 LEU 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 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 307 GLN ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7374 Z= 0.279 Angle : 0.669 8.970 10017 Z= 0.342 Chirality : 0.045 0.236 1155 Planarity : 0.005 0.067 1264 Dihedral : 8.694 96.713 1334 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.91 % Favored : 91.87 % Rotamer: Outliers : 4.28 % Allowed : 33.07 % 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: -0.67 (0.27), residues: 923 helix: 1.08 (0.31), residues: 269 sheet: -1.16 (0.43), residues: 132 loop : -1.08 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 163 HIS 0.010 0.001 HIS A 378 PHE 0.017 0.001 PHE A 552 TYR 0.017 0.002 TYR B 97 ARG 0.007 0.000 ARG A 276 ********************** 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 241 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 209 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.8411 (m-80) cc_final: 0.8042 (m-80) REVERT: A 310 ASP cc_start: 0.7646 (m-30) cc_final: 0.7397 (m-30) REVERT: A 345 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 400 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 431 LYS cc_start: 0.8352 (mtmt) cc_final: 0.8148 (mtmt) REVERT: A 514 GLN cc_start: 0.7604 (pm20) cc_final: 0.7029 (pm20) REVERT: A 599 MET cc_start: 0.6043 (pmm) cc_final: 0.4601 (pmm) REVERT: B 53 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7607 (ttpt) REVERT: B 205 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7735 (ptpp) REVERT: B 247 LEU cc_start: 0.7931 (tt) cc_final: 0.7648 (tp) REVERT: H 47 SER cc_start: 0.7968 (p) cc_final: 0.7641 (t) REVERT: H 89 SER cc_start: 0.8340 (p) cc_final: 0.7950 (m) REVERT: L 101 MET cc_start: 0.6616 (tmm) cc_final: 0.5900 (tmm) outliers start: 32 outliers final: 27 residues processed: 231 average time/residue: 0.1773 time to fit residues: 55.2710 Evaluate side-chains 240 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 400 THR 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 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 107 LEU 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 37 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN ** A 595 HIS ** 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 = 0.3731 r_free = 0.3731 target = 0.136928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122095 restraints weight = 10539.788| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.91 r_work: 0.3410 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7374 Z= 0.343 Angle : 0.703 9.991 10017 Z= 0.357 Chirality : 0.047 0.251 1155 Planarity : 0.005 0.066 1264 Dihedral : 8.704 94.750 1334 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.69 % Favored : 92.09 % Rotamer: Outliers : 4.55 % Allowed : 33.20 % Favored : 62.25 % 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: -0.78 (0.27), residues: 923 helix: 0.92 (0.30), residues: 270 sheet: -1.23 (0.43), residues: 131 loop : -1.10 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 163 HIS 0.012 0.002 HIS A 378 PHE 0.019 0.001 PHE A 552 TYR 0.017 0.002 TYR A 236 ARG 0.011 0.001 ARG A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.70 seconds wall clock time: 40 minutes 22.79 seconds (2422.79 seconds total)