Starting phenix.real_space_refine on Fri Jul 19 02:24:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qq0_18571/07_2024/8qq0_18571.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qq0_18571/07_2024/8qq0_18571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qq0_18571/07_2024/8qq0_18571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qq0_18571/07_2024/8qq0_18571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qq0_18571/07_2024/8qq0_18571.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qq0_18571/07_2024/8qq0_18571.cif" } resolution = 3.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 3632 2.51 5 N 920 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5677 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3751 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 28, 'TRANS': 455} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 814 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 928 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.45, per 1000 atoms: 1.14 Number of scatterers: 5677 At special positions: 0 Unit cell: (62.4, 88.14, 150.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1102 8.00 N 920 7.00 C 3632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG F 1 " - " NAG F 2 " " NAG a 1 " - " NAG a 2 " " NAG c 1 " - " NAG c 2 " " NAG e 1 " - " NAG e 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG c 1 " - " FUC c 3 " " NAG e 1 " - " FUC e 3 " NAG-ASN " NAG B 1 " - " ASN A 122 " " NAG F 1 " - " ASN A 331 " " NAG a 1 " - " ASN A 282 " " NAG c 1 " - " ASN A 343 " " NAG e 1 " - " ASN E 59 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.539A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.563A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.105A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.276A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.636A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.720A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.222A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.049A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.963A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 7.044A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.508A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 355 removed outlier: 4.116A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.770A pdb=" N ALA D 86 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.770A pdb=" N ALA D 86 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 17 through 18 Processing sheet with id=AB4, first strand: chain 'D' and resid 17 through 18 Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.601A pdb=" N ASN E 59 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1757 1.34 - 1.46: 1555 1.46 - 1.58: 2482 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5820 Sorted by residual: bond pdb=" C5 FUC F 3 " pdb=" O5 FUC F 3 " ideal model delta sigma weight residual 1.423 1.459 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG c 2 " pdb=" O5 NAG c 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 FUC F 3 " pdb=" O5 FUC F 3 " ideal model delta sigma weight residual 1.400 1.431 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" CG LEU A 223 " pdb=" CD2 LEU A 223 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 5815 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.71: 180 106.71 - 113.55: 3146 113.55 - 120.39: 2087 120.39 - 127.23: 2461 127.23 - 134.06: 61 Bond angle restraints: 7935 Sorted by residual: angle pdb=" CB LYS E 13 " pdb=" CG LYS E 13 " pdb=" CD LYS E 13 " ideal model delta sigma weight residual 111.30 118.49 -7.19 2.30e+00 1.89e-01 9.76e+00 angle pdb=" N VAL D 53 " pdb=" CA VAL D 53 " pdb=" C VAL D 53 " ideal model delta sigma weight residual 109.34 115.48 -6.14 2.08e+00 2.31e-01 8.71e+00 angle pdb=" C GLU D 52 " pdb=" N VAL D 53 " pdb=" CA VAL D 53 " ideal model delta sigma weight residual 121.97 127.14 -5.17 1.80e+00 3.09e-01 8.24e+00 angle pdb=" C VAL D 53 " pdb=" N THR D 54 " pdb=" CA THR D 54 " ideal model delta sigma weight residual 122.26 117.72 4.54 1.59e+00 3.96e-01 8.15e+00 angle pdb=" C GLY A 89 " pdb=" N VAL A 90 " pdb=" CA VAL A 90 " ideal model delta sigma weight residual 122.25 118.03 4.22 1.57e+00 4.06e-01 7.22e+00 ... (remaining 7930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 3285 23.88 - 47.76: 183 47.76 - 71.64: 44 71.64 - 95.52: 31 95.52 - 119.40: 20 Dihedral angle restraints: 3563 sinusoidal: 1498 harmonic: 2065 Sorted by residual: dihedral pdb=" CA GLU D 52 " pdb=" C GLU D 52 " pdb=" N VAL D 53 " pdb=" CA VAL D 53 " ideal model delta harmonic sigma weight residual 180.00 -132.68 -47.32 0 5.00e+00 4.00e-02 8.96e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.03 85.03 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 158.71 -65.71 1 1.00e+01 1.00e-02 5.65e+01 ... (remaining 3560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 603 0.042 - 0.084: 217 0.084 - 0.126: 82 0.126 - 0.168: 16 0.168 - 0.210: 5 Chirality restraints: 923 Sorted by residual: chirality pdb=" C4 NAG e 2 " pdb=" C3 NAG e 2 " pdb=" C5 NAG e 2 " pdb=" O4 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.32 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB THR E 119 " pdb=" CA THR E 119 " pdb=" OG1 THR E 119 " pdb=" CG2 THR E 119 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" C4 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" C5 NAG A1301 " pdb=" O4 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 920 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 217 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 463 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 45 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO D 46 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 46 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 46 " -0.023 5.00e-02 4.00e+02 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 237 2.71 - 3.26: 5083 3.26 - 3.80: 7599 3.80 - 4.35: 9611 4.35 - 4.90: 17645 Nonbonded interactions: 40175 Sorted by model distance: nonbonded pdb=" OG SER D 11 " pdb=" OG1 THR D 108 " model vdw 2.161 2.440 nonbonded pdb=" O CYS A 291 " pdb=" N ALA A 292 " model vdw 2.201 2.520 nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.213 2.520 nonbonded pdb=" NH1 ARG D 56 " pdb=" O VAL D 60 " model vdw 2.223 2.520 nonbonded pdb=" O SER D 65 " pdb=" OG1 THR D 76 " model vdw 2.258 2.440 ... (remaining 40170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'a' } ncs_group { reference = chain 'F' selection = chain 'c' selection = chain 'e' } 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 group one per residue 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: 12.680 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.005 0.049 5820 Z= 0.354 Angle : 0.786 7.187 7935 Z= 0.404 Chirality : 0.051 0.210 923 Planarity : 0.005 0.058 999 Dihedral : 20.439 119.400 2219 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.67 % Favored : 90.19 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.12 (0.28), residues: 693 helix: -4.03 (0.73), residues: 26 sheet: -0.62 (0.35), residues: 233 loop : -2.97 (0.23), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 50 HIS 0.005 0.002 HIS A 66 PHE 0.015 0.002 PHE A 238 TYR 0.022 0.002 TYR A 266 ARG 0.004 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.658 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1695 time to fit residues: 15.0737 Evaluate side-chains 55 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN E 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5820 Z= 0.226 Angle : 0.708 7.884 7935 Z= 0.337 Chirality : 0.049 0.218 923 Planarity : 0.004 0.043 999 Dihedral : 15.996 101.369 1052 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.50 % Favored : 92.35 % Rotamer: Outliers : 1.70 % Allowed : 9.18 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.92 (0.28), residues: 693 helix: -3.53 (0.71), residues: 28 sheet: -0.41 (0.35), residues: 225 loop : -2.86 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE A 238 TYR 0.012 0.001 TYR A 266 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.653 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 66 average time/residue: 0.1641 time to fit residues: 14.8561 Evaluate side-chains 65 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 0.0010 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 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 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5820 Z= 0.158 Angle : 0.642 8.708 7935 Z= 0.299 Chirality : 0.044 0.175 923 Planarity : 0.004 0.041 999 Dihedral : 10.896 79.991 1052 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.06 % Favored : 93.80 % Rotamer: Outliers : 2.21 % Allowed : 12.76 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.65 (0.28), residues: 693 helix: -2.77 (0.85), residues: 29 sheet: -0.13 (0.36), residues: 216 loop : -2.72 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.004 0.001 HIS A 66 PHE 0.009 0.001 PHE A 192 TYR 0.009 0.001 TYR A 204 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 55 time to evaluate : 0.652 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 64 average time/residue: 0.1621 time to fit residues: 14.2936 Evaluate side-chains 64 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5820 Z= 0.273 Angle : 0.678 8.452 7935 Z= 0.327 Chirality : 0.046 0.159 923 Planarity : 0.004 0.042 999 Dihedral : 8.887 61.182 1052 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.95 % Favored : 90.91 % Rotamer: Outliers : 3.57 % Allowed : 12.41 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.78 (0.29), residues: 693 helix: -2.57 (0.90), residues: 29 sheet: -0.40 (0.35), residues: 233 loop : -2.82 (0.24), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 50 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE A 92 TYR 0.014 0.002 TYR A 37 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.668 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 64 average time/residue: 0.1603 time to fit residues: 14.1826 Evaluate side-chains 69 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 51 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.0060 chunk 58 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5820 Z= 0.176 Angle : 0.607 8.154 7935 Z= 0.293 Chirality : 0.043 0.180 923 Planarity : 0.004 0.041 999 Dihedral : 7.789 56.726 1052 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.94 % Rotamer: Outliers : 3.57 % Allowed : 13.61 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.61 (0.29), residues: 693 helix: -2.49 (0.92), residues: 29 sheet: -0.15 (0.36), residues: 217 loop : -2.70 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 47 HIS 0.004 0.001 HIS A 66 PHE 0.008 0.001 PHE A 92 TYR 0.008 0.001 TYR A 204 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: E 60 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6453 (m-80) outliers start: 21 outliers final: 19 residues processed: 66 average time/residue: 0.1620 time to fit residues: 14.7191 Evaluate side-chains 69 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5820 Z= 0.236 Angle : 0.628 8.251 7935 Z= 0.308 Chirality : 0.044 0.149 923 Planarity : 0.004 0.041 999 Dihedral : 7.269 55.700 1052 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.37 % Favored : 91.49 % Rotamer: Outliers : 4.76 % Allowed : 13.78 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.69 (0.29), residues: 693 helix: -2.42 (0.94), residues: 29 sheet: -0.33 (0.35), residues: 224 loop : -2.72 (0.24), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS A 66 PHE 0.012 0.001 PHE A 92 TYR 0.011 0.001 TYR A 204 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 51 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: E 60 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6490 (m-80) outliers start: 28 outliers final: 26 residues processed: 71 average time/residue: 0.1611 time to fit residues: 15.7095 Evaluate side-chains 78 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 51 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5820 Z= 0.239 Angle : 0.623 8.209 7935 Z= 0.306 Chirality : 0.045 0.252 923 Planarity : 0.004 0.041 999 Dihedral : 7.073 55.843 1052 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.78 % Rotamer: Outliers : 4.93 % Allowed : 13.95 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.68 (0.29), residues: 693 helix: -2.36 (0.96), residues: 29 sheet: -0.38 (0.35), residues: 225 loop : -2.69 (0.24), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS A 66 PHE 0.011 0.001 PHE A 92 TYR 0.011 0.001 TYR A 265 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 50 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 60 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6505 (m-80) outliers start: 29 outliers final: 26 residues processed: 72 average time/residue: 0.1517 time to fit residues: 15.3186 Evaluate side-chains 77 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 50 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5820 Z= 0.164 Angle : 0.579 8.306 7935 Z= 0.282 Chirality : 0.043 0.147 923 Planarity : 0.004 0.040 999 Dihedral : 6.598 54.820 1052 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.27 % Allowed : 13.95 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.54 (0.29), residues: 693 helix: -2.39 (0.95), residues: 29 sheet: -0.21 (0.36), residues: 220 loop : -2.59 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS A 66 PHE 0.008 0.001 PHE A 192 TYR 0.009 0.001 TYR A 204 ARG 0.001 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 53 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 26 residues processed: 75 average time/residue: 0.1479 time to fit residues: 15.5181 Evaluate side-chains 78 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 52 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.0000 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.0000 chunk 56 optimal weight: 0.3980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5820 Z= 0.156 Angle : 0.570 8.500 7935 Z= 0.277 Chirality : 0.043 0.230 923 Planarity : 0.004 0.041 999 Dihedral : 6.267 54.336 1052 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.25 % Allowed : 14.97 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.40 (0.29), residues: 693 helix: -2.38 (0.95), residues: 29 sheet: -0.10 (0.36), residues: 220 loop : -2.50 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS A 66 PHE 0.009 0.001 PHE A 92 TYR 0.009 0.001 TYR A 204 ARG 0.001 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 54 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8358 (p0) cc_final: 0.8139 (p0) outliers start: 25 outliers final: 24 residues processed: 71 average time/residue: 0.1373 time to fit residues: 13.9520 Evaluate side-chains 73 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.0970 chunk 43 optimal weight: 0.0010 chunk 34 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5820 Z= 0.129 Angle : 0.559 8.529 7935 Z= 0.270 Chirality : 0.043 0.304 923 Planarity : 0.004 0.041 999 Dihedral : 6.001 54.101 1052 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.57 % Allowed : 15.48 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.21 (0.30), residues: 693 helix: -2.42 (0.94), residues: 29 sheet: 0.05 (0.36), residues: 220 loop : -2.36 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS A 66 PHE 0.010 0.001 PHE A 133 TYR 0.008 0.001 TYR A 204 ARG 0.003 0.000 ARG D 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: D 44 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7598 (mttt) REVERT: D 55 LYS cc_start: 0.8005 (ttmm) cc_final: 0.7723 (mtmt) outliers start: 21 outliers final: 21 residues processed: 67 average time/residue: 0.1447 time to fit residues: 13.7890 Evaluate side-chains 73 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 23 THR Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139459 restraints weight = 7239.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138548 restraints weight = 9711.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139154 restraints weight = 9443.257| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5820 Z= 0.213 Angle : 0.602 8.451 7935 Z= 0.293 Chirality : 0.043 0.147 923 Planarity : 0.004 0.041 999 Dihedral : 6.163 54.406 1052 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.42 % Allowed : 14.97 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.26 (0.30), residues: 693 helix: -2.37 (0.95), residues: 29 sheet: 0.02 (0.36), residues: 220 loop : -2.41 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 50 HIS 0.004 0.001 HIS A 66 PHE 0.014 0.001 PHE A 133 TYR 0.010 0.001 TYR A 265 ARG 0.002 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1948.32 seconds wall clock time: 35 minutes 29.32 seconds (2129.32 seconds total)