Starting phenix.real_space_refine on Thu Jul 2 22:48:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqo_23949/07_2026/7mqo_23949.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.171 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 94 5.16 5 C 6744 2.51 5 N 1800 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10642 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "F" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4883 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain breaks: 4 Chain: "E" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4883 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain breaks: 4 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 188 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 138 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "G" 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 chiralities: 2 Chain: "H" 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 chiralities: 2 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.39, per 1000 atoms: 0.22 Number of scatterers: 10642 At special positions: 0 Unit cell: (116.025, 137.865, 84.63, 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 94 16.00 O 2004 8.00 N 1800 7.00 C 6744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 11 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS B 7 " distance=1.92 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS B 19 " distance=1.99 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 435 " - pdb=" SG CYS F 468 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 26 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS E 188 " distance=2.03 Simple disulfide: pdb=" SG CYS E 192 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 196 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 208 " - pdb=" SG CYS E 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 237 " distance=2.02 Simple disulfide: pdb=" SG CYS E 241 " - pdb=" SG CYS E 253 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 284 " distance=2.04 Simple disulfide: pdb=" SG CYS E 266 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 308 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 333 " distance=2.03 Simple disulfide: pdb=" SG CYS E 435 " - pdb=" SG CYS E 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 11 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS D 7 " distance=2.14 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS D 19 " distance=2.07 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E1001 " - " ASN E 215 " " NAG E1002 " - " ASN E 418 " " NAG E1003 " - " ASN E 255 " " NAG E1004 " - " ASN E 16 " " NAG E1005 " - " ASN E 397 " " NAG E1006 " - " ASN E 25 " " NAG F1001 " - " ASN F 215 " " NAG F1002 " - " ASN F 418 " " NAG F1003 " - " ASN F 255 " " NAG F1004 " - " ASN F 16 " " NAG F1005 " - " ASN F 397 " " NAG F1006 " - " ASN F 25 " " NAG G 1 " - " ASN F 111 " " NAG H 1 " - " ASN E 111 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 254.2 milliseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 18 sheets defined 15.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.118A pdb=" N VAL B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.752A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN F 268 " --> pdb=" O HIS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 328 Processing helix chain 'F' and resid 351 through 358 Processing helix chain 'F' and resid 435 through 447 removed outlier: 3.650A pdb=" N ILE F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'F' and resid 693 through 714 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 255 through 269 removed outlier: 3.752A pdb=" N CYS E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN E 268 " --> pdb=" O HIS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 351 through 358 Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.651A pdb=" N ILE E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 498 No H-bonds generated for 'chain 'E' and resid 496 through 498' Processing helix chain 'E' and resid 693 through 714 Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'D' and resid 7 through 12 removed outlier: 4.117A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing sheet with id=AA1, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.440A pdb=" N LEU F 33 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 232 through 233 Processing sheet with id=AA4, first strand: chain 'F' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'F' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'F' and resid 311 through 313 removed outlier: 3.623A pdb=" N ASN F 337 " --> pdb=" O CYS F 312 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 368 through 370 removed outlier: 6.791A pdb=" N PHE F 400 " --> pdb=" O PHE F 427 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 475 through 480 removed outlier: 6.556A pdb=" N ARG F 488 " --> pdb=" O SER F 476 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE F 478 " --> pdb=" O LEU F 486 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU F 486 " --> pdb=" O ILE F 478 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE F 485 " --> pdb=" O MET F 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET F 553 " --> pdb=" O ILE F 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 530 through 534 removed outlier: 3.610A pdb=" N THR F 530 " --> pdb=" O TYR F 507 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR F 507 " --> pdb=" O THR F 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 502 " --> pdb=" O LEU F 569 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 567 " --> pdb=" O MET F 504 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 565 " --> pdb=" O PHE F 506 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 563 " --> pdb=" O LYS F 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.439A pdb=" N LEU E 33 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU E 93 " --> pdb=" O ARG E 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 232 through 233 Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 248 Processing sheet with id=AB5, first strand: chain 'E' and resid 292 through 294 Processing sheet with id=AB6, first strand: chain 'E' and resid 311 through 313 removed outlier: 3.624A pdb=" N ASN E 337 " --> pdb=" O CYS E 312 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 370 removed outlier: 6.791A pdb=" N PHE E 400 " --> pdb=" O PHE E 427 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 475 through 480 removed outlier: 6.556A pdb=" N ARG E 488 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE E 478 " --> pdb=" O LEU E 486 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU E 486 " --> pdb=" O ILE E 478 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE E 485 " --> pdb=" O MET E 553 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET E 553 " --> pdb=" O ILE E 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 530 through 534 removed outlier: 3.611A pdb=" N THR E 530 " --> pdb=" O TYR E 507 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR E 507 " --> pdb=" O THR E 530 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY E 502 " --> pdb=" O LEU E 569 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 567 " --> pdb=" O MET E 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE E 565 " --> pdb=" O PHE E 506 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 563 " --> pdb=" O LYS E 508 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 483 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: 1.51 Time building geometry restraints manager: 1.16 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: 3420 1.34 - 1.46: 2464 1.46 - 1.58: 4886 1.58 - 1.70: 2 1.70 - 1.82: 112 Bond restraints: 10884 Sorted by residual: bond pdb=" C1 NAG F1002 " pdb=" O5 NAG F1002 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" CG PRO E 222 " pdb=" CD PRO E 222 " ideal model delta sigma weight residual 1.503 1.426 0.077 3.40e-02 8.65e+02 5.07e+00 bond pdb=" CG PRO F 222 " pdb=" CD PRO F 222 " ideal model delta sigma weight residual 1.503 1.427 0.076 3.40e-02 8.65e+02 4.97e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 10879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 13932 1.45 - 2.90: 657 2.90 - 4.35: 117 4.35 - 5.80: 34 5.80 - 7.25: 2 Bond angle restraints: 14742 Sorted by residual: angle pdb=" N PRO E 222 " pdb=" CD PRO E 222 " pdb=" CG PRO E 222 " ideal model delta sigma weight residual 103.20 95.95 7.25 1.50e+00 4.44e-01 2.34e+01 angle pdb=" N PRO F 222 " pdb=" CD PRO F 222 " pdb=" CG PRO F 222 " ideal model delta sigma weight residual 103.20 95.98 7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" N GLU F 22 " pdb=" CA GLU F 22 " pdb=" C GLU F 22 " ideal model delta sigma weight residual 113.01 107.88 5.13 1.20e+00 6.94e-01 1.83e+01 angle pdb=" N GLU E 22 " pdb=" CA GLU E 22 " pdb=" C GLU E 22 " ideal model delta sigma weight residual 113.01 107.89 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" N ALA D 14 " pdb=" CA ALA D 14 " pdb=" C ALA D 14 " ideal model delta sigma weight residual 113.55 108.74 4.81 1.26e+00 6.30e-01 1.46e+01 ... (remaining 14737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 5725 17.69 - 35.39: 592 35.39 - 53.08: 153 53.08 - 70.77: 20 70.77 - 88.47: 10 Dihedral angle restraints: 6500 sinusoidal: 2734 harmonic: 3766 Sorted by residual: dihedral pdb=" CB CYS F 259 " pdb=" SG CYS F 259 " pdb=" SG CYS F 284 " pdb=" CB CYS F 284 " ideal model delta sinusoidal sigma weight residual -86.00 -152.96 66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS E 259 " pdb=" SG CYS E 259 " pdb=" SG CYS E 284 " pdb=" CB CYS E 284 " ideal model delta sinusoidal sigma weight residual -86.00 -152.90 66.90 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS F 8 " pdb=" SG CYS F 8 " pdb=" SG CYS F 26 " pdb=" CB CYS F 26 " ideal model delta sinusoidal sigma weight residual 93.00 156.57 -63.57 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 6497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1301 0.056 - 0.111: 299 0.111 - 0.167: 56 0.167 - 0.222: 4 0.222 - 0.278: 2 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C1 NAG E1002 " pdb=" ND2 ASN E 418 " pdb=" C2 NAG E1002 " pdb=" O5 NAG E1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1 NAG F1002 " pdb=" ND2 ASN F 418 " pdb=" C2 NAG F1002 " pdb=" O5 NAG F1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C4 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C5 NAG H 1 " pdb=" O4 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 1659 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 8 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO F 9 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO F 9 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 9 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 8 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO E 9 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 9 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 9 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 221 " -0.043 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO E 222 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 222 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 222 " -0.035 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 100 2.60 - 3.18: 9047 3.18 - 3.75: 14987 3.75 - 4.33: 21678 4.33 - 4.90: 35591 Nonbonded interactions: 81403 Sorted by model distance: nonbonded pdb=" OE2 GLU F 443 " pdb=" NE2 GLN F 452 " model vdw 2.030 3.120 nonbonded pdb=" OE2 GLU E 443 " pdb=" NE2 GLN E 452 " model vdw 2.031 3.120 nonbonded pdb=" OD1 ASP F 12 " pdb=" NE2 GLN F 34 " model vdw 2.158 3.120 nonbonded pdb=" OD1 ASP E 12 " pdb=" NE2 GLN E 34 " model vdw 2.159 3.120 nonbonded pdb=" O ILE E 29 " pdb=" OG1 THR E 58 " model vdw 2.268 3.040 ... (remaining 81398 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.106 10938 Z= 0.203 Angle : 0.768 11.492 14866 Z= 0.403 Chirality : 0.049 0.278 1662 Planarity : 0.005 0.064 1874 Dihedral : 14.909 88.468 3950 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 13.10 % Favored : 86.75 % Rotamer: Outliers : 0.17 % Allowed : 0.76 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.22), residues: 1260 helix: 0.25 (0.39), residues: 188 sheet: -2.53 (0.49), residues: 106 loop : -2.50 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 488 TYR 0.019 0.001 TYR E 430 PHE 0.017 0.002 PHE E 427 TRP 0.012 0.001 TRP F 251 HIS 0.007 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (10884) covalent geometry : angle 0.71348 / 0.39 (14742) SS BOND : bond 0.02616 / 1.39 ( 38) SS BOND : angle 2.73399 / 1.70 ( 76) hydrogen bonds : bond 0.21951 / 13.89 ( 177) hydrogen bonds : angle 8.41841 / 5.91 ( 483) link_BETA1-4 : bond 0.00021 / 0.01 ( 2) link_BETA1-4 : angle 4.90747 / 2.20 ( 6) link_NAG-ASN : bond 0.00591 / 0.44 ( 14) link_NAG-ASN : angle 3.58674 / 2.15 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 372 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.6729 (mtp85) REVERT: E 372 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6595 (mtp85) REVERT: C 10 ILE cc_start: 0.8518 (mt) cc_final: 0.8309 (mt) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.0950 time to fit residues: 20.4360 Evaluate side-chains 122 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN E 15 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.211832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.190153 restraints weight = 11229.915| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.38 r_work: 0.3498 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10938 Z= 0.213 Angle : 0.720 6.367 14866 Z= 0.367 Chirality : 0.049 0.226 1662 Planarity : 0.005 0.045 1874 Dihedral : 6.016 47.882 1403 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.46 % Favored : 87.38 % Rotamer: Outliers : 0.93 % Allowed : 9.71 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.22), residues: 1260 helix: 0.28 (0.39), residues: 178 sheet: -2.29 (0.48), residues: 118 loop : -2.61 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 409 TYR 0.015 0.002 TYR F 512 PHE 0.020 0.002 PHE E 427 TRP 0.012 0.001 TRP F 251 HIS 0.006 0.001 HIS F 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (10884) covalent geometry : angle 0.70611 / 0.36 (14742) SS BOND : bond 0.00332 / 0.21 ( 38) SS BOND : angle 1.20501 / 0.81 ( 76) hydrogen bonds : bond 0.05478 / 3.75 ( 177) hydrogen bonds : angle 6.68634 / 4.63 ( 483) link_BETA1-4 : bond 0.00108 / 0.06 ( 2) link_BETA1-4 : angle 3.50279 / 1.64 ( 6) link_NAG-ASN : bond 0.00529 / 0.39 ( 14) link_NAG-ASN : angle 2.08325 / 1.25 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8640 (mt) cc_final: 0.8377 (mt) REVERT: F 250 ASP cc_start: 0.8142 (t0) cc_final: 0.7930 (t0) REVERT: F 294 MET cc_start: 0.6716 (ttt) cc_final: 0.6234 (tpt) REVERT: F 342 ILE cc_start: 0.8559 (pt) cc_final: 0.8317 (mt) REVERT: E 131 ILE cc_start: 0.8627 (mt) cc_final: 0.8372 (mt) REVERT: E 294 MET cc_start: 0.6666 (ttt) cc_final: 0.6449 (tpt) REVERT: E 342 ILE cc_start: 0.8560 (pt) cc_final: 0.8306 (mt) REVERT: E 416 LYS cc_start: 0.7530 (pmtt) cc_final: 0.7282 (pmtt) outliers start: 11 outliers final: 8 residues processed: 155 average time/residue: 0.0966 time to fit residues: 22.1018 Evaluate side-chains 140 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain E residue 15 ASN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 238 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 108 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.198269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.146648 restraints weight = 11384.852| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.42 r_work: 0.3523 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10938 Z= 0.133 Angle : 0.623 6.285 14866 Z= 0.320 Chirality : 0.045 0.172 1662 Planarity : 0.004 0.041 1874 Dihedral : 5.490 28.632 1400 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.90 % Favored : 87.94 % Rotamer: Outliers : 1.18 % Allowed : 11.91 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.22), residues: 1260 helix: 0.80 (0.40), residues: 168 sheet: -1.89 (0.52), residues: 106 loop : -2.57 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 409 TYR 0.011 0.001 TYR F 512 PHE 0.014 0.001 PHE E 565 TRP 0.009 0.001 TRP E 251 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (10884) covalent geometry : angle 0.60708 / 0.32 (14742) SS BOND : bond 0.00219 / 0.14 ( 38) SS BOND : angle 1.24348 / 0.89 ( 76) hydrogen bonds : bond 0.04412 / 3.08 ( 177) hydrogen bonds : angle 6.28862 / 4.39 ( 483) link_BETA1-4 : bond 0.00109 / 0.06 ( 2) link_BETA1-4 : angle 3.78896 / 1.73 ( 6) link_NAG-ASN : bond 0.00401 / 0.28 ( 14) link_NAG-ASN : angle 1.81715 / 1.09 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8624 (mt) cc_final: 0.8386 (mt) REVERT: F 250 ASP cc_start: 0.8248 (t0) cc_final: 0.8013 (t0) REVERT: F 256 PHE cc_start: 0.7709 (t80) cc_final: 0.7307 (t80) REVERT: F 260 GLN cc_start: 0.6688 (mt0) cc_final: 0.6202 (mt0) REVERT: F 294 MET cc_start: 0.6991 (ttt) cc_final: 0.6546 (tpt) REVERT: F 342 ILE cc_start: 0.8545 (pt) cc_final: 0.8250 (mp) REVERT: F 444 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7763 (mt-10) REVERT: E 131 ILE cc_start: 0.8627 (mt) cc_final: 0.8388 (mt) REVERT: E 151 ASP cc_start: 0.7462 (m-30) cc_final: 0.7260 (m-30) REVERT: E 189 GLN cc_start: 0.5918 (tm-30) cc_final: 0.5585 (tm-30) REVERT: E 256 PHE cc_start: 0.7680 (t80) cc_final: 0.7437 (t80) REVERT: E 294 MET cc_start: 0.6694 (ttt) cc_final: 0.6147 (tpt) REVERT: E 342 ILE cc_start: 0.8523 (pt) cc_final: 0.8201 (mp) REVERT: E 444 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7780 (mt-10) REVERT: C 10 ILE cc_start: 0.8591 (mt) cc_final: 0.8367 (mt) outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.0920 time to fit residues: 19.1403 Evaluate side-chains 131 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.196349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.141968 restraints weight = 11377.851| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.38 r_work: 0.3358 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10938 Z= 0.143 Angle : 0.615 5.500 14866 Z= 0.316 Chirality : 0.045 0.186 1662 Planarity : 0.004 0.044 1874 Dihedral : 5.346 27.702 1400 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.94 % Allowed : 13.34 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.22), residues: 1260 helix: 0.95 (0.41), residues: 166 sheet: -1.98 (0.50), residues: 110 loop : -2.55 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 409 TYR 0.010 0.001 TYR F 512 PHE 0.013 0.001 PHE F 382 TRP 0.011 0.001 TRP E 251 HIS 0.003 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (10884) covalent geometry : angle 0.60360 / 0.31 (14742) SS BOND : bond 0.00255 / 0.17 ( 38) SS BOND : angle 0.96114 / 0.68 ( 76) hydrogen bonds : bond 0.03998 / 2.79 ( 177) hydrogen bonds : angle 6.04089 / 4.22 ( 483) link_BETA1-4 : bond 0.00059 / 0.03 ( 2) link_BETA1-4 : angle 3.34055 / 1.53 ( 6) link_NAG-ASN : bond 0.00351 / 0.26 ( 14) link_NAG-ASN : angle 1.69418 / 1.04 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: F 131 ILE cc_start: 0.8476 (mt) cc_final: 0.8232 (mt) REVERT: F 250 ASP cc_start: 0.8333 (t0) cc_final: 0.8115 (t0) REVERT: F 358 LEU cc_start: 0.8027 (tp) cc_final: 0.7764 (tp) REVERT: E 12 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: E 131 ILE cc_start: 0.8520 (mt) cc_final: 0.8290 (mt) REVERT: E 151 ASP cc_start: 0.6836 (m-30) cc_final: 0.6616 (m-30) REVERT: E 250 ASP cc_start: 0.8411 (t0) cc_final: 0.8202 (t0) REVERT: E 358 LEU cc_start: 0.7939 (tp) cc_final: 0.7663 (tp) REVERT: E 416 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7165 (pmtt) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.0979 time to fit residues: 20.0758 Evaluate side-chains 137 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.217986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.187492 restraints weight = 11267.503| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.91 r_work: 0.3702 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10938 Z= 0.130 Angle : 0.595 5.508 14866 Z= 0.305 Chirality : 0.044 0.190 1662 Planarity : 0.004 0.045 1874 Dihedral : 5.239 28.661 1400 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.54 % Favored : 87.46 % Rotamer: Outliers : 1.94 % Allowed : 15.46 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.22), residues: 1260 helix: 1.01 (0.41), residues: 166 sheet: -1.78 (0.51), residues: 110 loop : -2.54 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 409 TYR 0.010 0.001 TYR F 507 PHE 0.013 0.001 PHE F 705 TRP 0.009 0.001 TRP E 251 HIS 0.003 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10884) covalent geometry : angle 0.58425 / 0.30 (14742) SS BOND : bond 0.00224 / 0.15 ( 38) SS BOND : angle 0.79066 / 0.55 ( 76) hydrogen bonds : bond 0.03855 / 2.70 ( 177) hydrogen bonds : angle 5.91928 / 4.15 ( 483) link_BETA1-4 : bond 0.00055 / 0.03 ( 2) link_BETA1-4 : angle 3.30924 / 1.51 ( 6) link_NAG-ASN : bond 0.00354 / 0.25 ( 14) link_NAG-ASN : angle 1.61664 / 1.00 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8807 (mt) cc_final: 0.8583 (mt) REVERT: E 12 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: E 131 ILE cc_start: 0.8823 (mt) cc_final: 0.8606 (mt) REVERT: E 342 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8226 (mp) outliers start: 23 outliers final: 17 residues processed: 138 average time/residue: 0.0968 time to fit residues: 19.6548 Evaluate side-chains 132 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.212492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.191136 restraints weight = 11174.162| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.33 r_work: 0.3547 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10938 Z= 0.110 Angle : 0.586 5.367 14866 Z= 0.302 Chirality : 0.044 0.188 1662 Planarity : 0.004 0.046 1874 Dihedral : 5.129 27.463 1400 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 1.86 % Allowed : 16.05 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.22), residues: 1260 helix: 1.15 (0.41), residues: 166 sheet: -1.68 (0.51), residues: 110 loop : -2.53 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 409 TYR 0.012 0.001 TYR F 507 PHE 0.018 0.001 PHE E 256 TRP 0.008 0.001 TRP F 412 HIS 0.003 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10884) covalent geometry : angle 0.57371 / 0.30 (14742) SS BOND : bond 0.00216 / 0.15 ( 38) SS BOND : angle 1.09773 / 0.72 ( 76) hydrogen bonds : bond 0.03555 / 2.50 ( 177) hydrogen bonds : angle 5.82608 / 4.12 ( 483) link_BETA1-4 : bond 0.00149 / 0.09 ( 2) link_BETA1-4 : angle 3.19973 / 1.45 ( 6) link_NAG-ASN : bond 0.00340 / 0.23 ( 14) link_NAG-ASN : angle 1.58198 / 0.99 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: F 131 ILE cc_start: 0.8706 (mt) cc_final: 0.8485 (mt) REVERT: E 131 ILE cc_start: 0.8698 (mt) cc_final: 0.8489 (mt) outliers start: 22 outliers final: 17 residues processed: 137 average time/residue: 0.0971 time to fit residues: 19.4829 Evaluate side-chains 128 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.213111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186879 restraints weight = 11159.795| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.65 r_work: 0.3466 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10938 Z= 0.163 Angle : 0.634 5.780 14866 Z= 0.325 Chirality : 0.046 0.192 1662 Planarity : 0.004 0.044 1874 Dihedral : 5.379 27.889 1400 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 3.12 % Allowed : 15.20 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.22), residues: 1260 helix: 1.01 (0.41), residues: 166 sheet: -1.70 (0.50), residues: 110 loop : -2.57 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 409 TYR 0.011 0.001 TYR F 60 PHE 0.015 0.002 PHE E 382 TRP 0.023 0.001 TRP E 183 HIS 0.005 0.001 HIS E 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (10884) covalent geometry : angle 0.62141 / 0.32 (14742) SS BOND : bond 0.00275 / 0.18 ( 38) SS BOND : angle 1.23887 / 0.96 ( 76) hydrogen bonds : bond 0.04019 / 2.82 ( 177) hydrogen bonds : angle 5.92708 / 4.20 ( 483) link_BETA1-4 : bond 0.00011 / 0.01 ( 2) link_BETA1-4 : angle 3.10654 / 1.43 ( 6) link_NAG-ASN : bond 0.00302 / 0.22 ( 14) link_NAG-ASN : angle 1.60195 / 0.98 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: F 131 ILE cc_start: 0.8823 (mt) cc_final: 0.8470 (mt) REVERT: E 342 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8295 (mp) outliers start: 37 outliers final: 25 residues processed: 159 average time/residue: 0.0942 time to fit residues: 22.0152 Evaluate side-chains 148 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN E 405 ASN C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.216579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.180765 restraints weight = 11275.455| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.83 r_work: 0.3598 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10938 Z= 0.157 Angle : 0.648 8.565 14866 Z= 0.331 Chirality : 0.046 0.199 1662 Planarity : 0.004 0.048 1874 Dihedral : 5.407 27.886 1400 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.30 % Favored : 87.62 % Rotamer: Outliers : 3.04 % Allowed : 16.05 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.22), residues: 1260 helix: 1.04 (0.41), residues: 166 sheet: -1.62 (0.52), residues: 110 loop : -2.58 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 409 TYR 0.012 0.001 TYR F 507 PHE 0.016 0.002 PHE E 256 TRP 0.020 0.001 TRP F 183 HIS 0.007 0.001 HIS D 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (10884) covalent geometry : angle 0.63764 / 0.33 (14742) SS BOND : bond 0.00248 / 0.17 ( 38) SS BOND : angle 1.11355 / 0.85 ( 76) hydrogen bonds : bond 0.03984 / 2.80 ( 177) hydrogen bonds : angle 6.07913 / 4.18 ( 483) link_BETA1-4 : bond 0.00060 / 0.04 ( 2) link_BETA1-4 : angle 3.14508 / 1.44 ( 6) link_NAG-ASN : bond 0.00318 / 0.23 ( 14) link_NAG-ASN : angle 1.54881 / 0.93 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: E 280 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.8075 (t-90) REVERT: E 342 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8303 (mp) outliers start: 36 outliers final: 30 residues processed: 153 average time/residue: 0.0893 time to fit residues: 20.3799 Evaluate side-chains 151 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 280 HIS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 108 ASN F 417 HIS F 429 HIS F 431 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 HIS E 431 ASN C 21 HIS C 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.209970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181852 restraints weight = 11198.290| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.13 r_work: 0.3605 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10938 Z= 0.224 Angle : 0.718 13.289 14866 Z= 0.365 Chirality : 0.048 0.195 1662 Planarity : 0.005 0.040 1874 Dihedral : 5.565 28.417 1400 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.81 % Favored : 86.11 % Rotamer: Outliers : 2.96 % Allowed : 16.22 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.22), residues: 1260 helix: 0.99 (0.41), residues: 160 sheet: -1.59 (0.52), residues: 110 loop : -2.65 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 409 TYR 0.016 0.002 TYR E 127 PHE 0.020 0.002 PHE F 427 TRP 0.009 0.002 TRP F 489 HIS 0.009 0.001 HIS F 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.22 (10884) covalent geometry : angle 0.70739 / 0.36 (14742) SS BOND : bond 0.00297 / 0.19 ( 38) SS BOND : angle 1.17829 / 0.89 ( 76) hydrogen bonds : bond 0.04526 / 3.17 ( 177) hydrogen bonds : angle 6.11598 / 4.21 ( 483) link_BETA1-4 : bond 0.00155 / 0.09 ( 2) link_BETA1-4 : angle 3.11988 / 1.43 ( 6) link_NAG-ASN : bond 0.00296 / 0.22 ( 14) link_NAG-ASN : angle 1.66353 / 1.03 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: E 280 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (t-90) REVERT: E 342 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8436 (mp) outliers start: 35 outliers final: 30 residues processed: 150 average time/residue: 0.0992 time to fit residues: 21.7302 Evaluate side-chains 151 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 159 CYS Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 405 ASN Chi-restraints excluded: chain F residue 429 HIS Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 280 HIS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 405 ASN Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 405 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.218111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.195249 restraints weight = 11185.843| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.18 r_work: 0.3557 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10938 Z= 0.122 Angle : 0.651 13.635 14866 Z= 0.331 Chirality : 0.045 0.192 1662 Planarity : 0.004 0.054 1874 Dihedral : 5.348 28.074 1400 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.90 % Favored : 88.02 % Rotamer: Outliers : 2.45 % Allowed : 16.81 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.22), residues: 1260 helix: 1.31 (0.42), residues: 160 sheet: -1.48 (0.54), residues: 110 loop : -2.59 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 409 TYR 0.018 0.001 TYR F 430 PHE 0.033 0.002 PHE F 428 TRP 0.015 0.001 TRP F 183 HIS 0.006 0.001 HIS F 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (10884) covalent geometry : angle 0.64258 / 0.33 (14742) SS BOND : bond 0.00212 / 0.15 ( 38) SS BOND : angle 0.90668 / 0.67 ( 76) hydrogen bonds : bond 0.03676 / 2.59 ( 177) hydrogen bonds : angle 5.91540 / 4.10 ( 483) link_BETA1-4 : bond 0.00133 / 0.08 ( 2) link_BETA1-4 : angle 3.13784 / 1.42 ( 6) link_NAG-ASN : bond 0.00342 / 0.24 ( 14) link_NAG-ASN : angle 1.49063 / 0.91 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: F 239 GLU cc_start: 0.7580 (tp30) cc_final: 0.7279 (mm-30) REVERT: F 717 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7972 (tpt170) REVERT: E 151 ASP cc_start: 0.7306 (m-30) cc_final: 0.6956 (m-30) REVERT: E 280 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.8047 (t-90) REVERT: E 342 ILE cc_start: 0.8494 (pt) cc_final: 0.8266 (mp) REVERT: E 358 LEU cc_start: 0.8236 (tp) cc_final: 0.7824 (tp) outliers start: 29 outliers final: 23 residues processed: 150 average time/residue: 0.0912 time to fit residues: 20.2192 Evaluate side-chains 144 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 266 CYS Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 381 PHE Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 280 HIS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 381 PHE Chi-restraints excluded: chain E residue 531 VAL Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 90 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 5 optimal weight: 0.0030 chunk 124 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 HIS E 108 ASN ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS C 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.216588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.193702 restraints weight = 11142.482| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.18 r_work: 0.3830 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10938 Z= 0.117 Angle : 0.626 13.487 14866 Z= 0.317 Chirality : 0.044 0.192 1662 Planarity : 0.004 0.048 1874 Dihedral : 5.230 26.904 1400 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.54 % Favored : 87.38 % Rotamer: Outliers : 2.36 % Allowed : 17.48 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1260 helix: 1.43 (0.42), residues: 160 sheet: -1.32 (0.54), residues: 110 loop : -2.59 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 409 TYR 0.009 0.001 TYR F 507 PHE 0.016 0.001 PHE F 705 TRP 0.014 0.002 TRP F 133 HIS 0.005 0.001 HIS F 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10884) covalent geometry : angle 0.61827 / 0.32 (14742) SS BOND : bond 0.00210 / 0.15 ( 38) SS BOND : angle 0.79098 / 0.58 ( 76) hydrogen bonds : bond 0.03453 / 2.43 ( 177) hydrogen bonds : angle 5.75126 / 3.99 ( 483) link_BETA1-4 : bond 0.00144 / 0.09 ( 2) link_BETA1-4 : angle 3.02805 / 1.36 ( 6) link_NAG-ASN : bond 0.00317 / 0.23 ( 14) link_NAG-ASN : angle 1.47611 / 0.91 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.97 seconds wall clock time: 45 minutes 2.04 seconds (2702.04 seconds total)