Starting phenix.real_space_refine on Wed Mar 4 04:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqo_23949/03_2026/7mqo_23949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqo_23949/03_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_23949/03_2026/7mqo_23949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqo_23949/03_2026/7mqo_23949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqo_23949/03_2026/7mqo_23949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqo_23949/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.29, 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: 0.83 Conformation dependent library (CDL) restraints added in 516.4 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: 0.27 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: 1.44 Time building geometry restraints manager: 1.20 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: 6041 17.69 - 35.39: 604 35.39 - 53.08: 155 53.08 - 70.77: 26 70.77 - 88.47: 10 Dihedral angle restraints: 6836 sinusoidal: 3070 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 6833 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 14.608 88.468 4286 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 covalent geometry : bond 0.00430 (10884) covalent geometry : angle 0.71348 (14742) SS BOND : bond 0.02616 ( 38) SS BOND : angle 2.73399 ( 76) hydrogen bonds : bond 0.21951 ( 177) hydrogen bonds : angle 8.41841 ( 483) link_BETA1-4 : bond 0.00021 ( 2) link_BETA1-4 : angle 4.90747 ( 6) link_NAG-ASN : bond 0.00591 ( 14) link_NAG-ASN : angle 3.58674 ( 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 : 0.409 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: 0.1011 time to fit residues: 21.6781 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 : 0.402 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.208459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.176627 restraints weight = 11206.430| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.32 r_work: 0.3378 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1657 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= 0.212 Angle : 0.739 6.695 14866 Z= 0.375 Chirality : 0.049 0.209 1662 Planarity : 0.005 0.046 1874 Dihedral : 6.765 48.300 1739 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.86 % Favored : 86.98 % Rotamer: Outliers : 1.01 % Allowed : 9.97 % Favored : 89.02 % 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: -3.01 (0.22), residues: 1260 helix: 0.21 (0.39), residues: 178 sheet: -2.36 (0.48), residues: 118 loop : -2.61 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 409 TYR 0.016 0.002 TYR F 512 PHE 0.020 0.002 PHE E 427 TRP 0.012 0.002 TRP F 251 HIS 0.007 0.001 HIS E 440 Details of bonding type rmsd covalent geometry : bond 0.00515 (10884) covalent geometry : angle 0.72398 (14742) SS BOND : bond 0.00300 ( 38) SS BOND : angle 1.22205 ( 76) hydrogen bonds : bond 0.05141 ( 177) hydrogen bonds : angle 6.64665 ( 483) link_BETA1-4 : bond 0.00077 ( 2) link_BETA1-4 : angle 3.85478 ( 6) link_NAG-ASN : bond 0.00713 ( 14) link_NAG-ASN : angle 2.09130 ( 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 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8575 (mt) cc_final: 0.8321 (mt) REVERT: F 250 ASP cc_start: 0.8149 (t0) cc_final: 0.7911 (t0) REVERT: F 277 TYR cc_start: 0.6585 (m-80) cc_final: 0.6346 (m-80) REVERT: F 294 MET cc_start: 0.6672 (ttt) cc_final: 0.6185 (tpt) REVERT: F 342 ILE cc_start: 0.8559 (pt) cc_final: 0.8292 (mp) REVERT: F 416 LYS cc_start: 0.7482 (pttt) cc_final: 0.7252 (pmtt) REVERT: E 131 ILE cc_start: 0.8575 (mt) cc_final: 0.8315 (mt) REVERT: E 250 ASP cc_start: 0.8172 (t0) cc_final: 0.7930 (t0) REVERT: E 294 MET cc_start: 0.6612 (ttt) cc_final: 0.6351 (tpt) REVERT: E 342 ILE cc_start: 0.8591 (pt) cc_final: 0.8285 (mp) REVERT: E 416 LYS cc_start: 0.7489 (pttt) cc_final: 0.7160 (pmtt) outliers start: 12 outliers final: 7 residues processed: 157 average time/residue: 0.0876 time to fit residues: 20.5003 Evaluate side-chains 139 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 37 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 GLN ** 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 = 0.4111 r_free = 0.4111 target = 0.195869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143468 restraints weight = 11381.332| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.48 r_work: 0.3407 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10938 Z= 0.164 Angle : 0.645 6.543 14866 Z= 0.332 Chirality : 0.046 0.171 1662 Planarity : 0.004 0.041 1874 Dihedral : 6.391 50.627 1736 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.78 % Favored : 87.06 % Rotamer: Outliers : 1.52 % Allowed : 11.49 % Favored : 86.99 % 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: -2.86 (0.22), residues: 1260 helix: 0.76 (0.40), residues: 166 sheet: -1.98 (0.51), residues: 106 loop : -2.61 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 409 TYR 0.011 0.001 TYR F 512 PHE 0.015 0.002 PHE F 382 TRP 0.009 0.001 TRP E 251 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00400 (10884) covalent geometry : angle 0.62957 (14742) SS BOND : bond 0.00372 ( 38) SS BOND : angle 1.15530 ( 76) hydrogen bonds : bond 0.04653 ( 177) hydrogen bonds : angle 6.29273 ( 483) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 4.03998 ( 6) link_NAG-ASN : bond 0.00406 ( 14) link_NAG-ASN : angle 1.85324 ( 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 154 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 131 ILE cc_start: 0.8607 (mt) cc_final: 0.8357 (mt) REVERT: F 151 ASP cc_start: 0.7210 (m-30) cc_final: 0.6972 (m-30) REVERT: F 256 PHE cc_start: 0.7677 (t80) cc_final: 0.7264 (t80) REVERT: F 260 GLN cc_start: 0.6739 (mt0) cc_final: 0.6223 (mt0) REVERT: F 294 MET cc_start: 0.7043 (ttt) cc_final: 0.6532 (tpt) REVERT: F 342 ILE cc_start: 0.8564 (pt) cc_final: 0.8272 (mp) REVERT: F 416 LYS cc_start: 0.7424 (pttt) cc_final: 0.7165 (pmtt) REVERT: E 131 ILE cc_start: 0.8612 (mt) cc_final: 0.8357 (mt) REVERT: E 151 ASP cc_start: 0.7265 (m-30) cc_final: 0.7034 (m-30) REVERT: E 189 GLN cc_start: 0.6005 (tm-30) cc_final: 0.5609 (tm-30) REVERT: E 250 ASP cc_start: 0.8316 (t0) cc_final: 0.8060 (t0) REVERT: E 342 ILE cc_start: 0.8576 (pt) cc_final: 0.8265 (mp) REVERT: E 416 LYS cc_start: 0.7505 (pttt) cc_final: 0.7164 (pmtt) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.0918 time to fit residues: 20.2830 Evaluate side-chains 136 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 489 TRP Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain F residue 561 GLN Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 489 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.0020 chunk 118 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4125 r_free = 0.4125 target = 0.196598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142832 restraints weight = 11322.505| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.35 r_work: 0.3366 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2200 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= 0.129 Angle : 0.606 6.299 14866 Z= 0.312 Chirality : 0.044 0.158 1662 Planarity : 0.004 0.041 1874 Dihedral : 6.256 51.454 1736 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 1.35 % Allowed : 13.85 % Favored : 84.80 % 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: -2.80 (0.22), residues: 1260 helix: 0.88 (0.41), residues: 166 sheet: -1.95 (0.50), residues: 110 loop : -2.59 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 409 TYR 0.009 0.001 TYR E 512 PHE 0.015 0.001 PHE F 705 TRP 0.008 0.001 TRP F 251 HIS 0.004 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00311 (10884) covalent geometry : angle 0.59315 (14742) SS BOND : bond 0.00246 ( 38) SS BOND : angle 0.89046 ( 76) hydrogen bonds : bond 0.03968 ( 177) hydrogen bonds : angle 6.05013 ( 483) link_BETA1-4 : bond 0.00097 ( 2) link_BETA1-4 : angle 3.77348 ( 6) link_NAG-ASN : bond 0.00390 ( 14) link_NAG-ASN : angle 1.77893 ( 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 142 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7856 (mm-30) REVERT: F 12 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: F 131 ILE cc_start: 0.8475 (mt) cc_final: 0.8219 (mt) REVERT: F 342 ILE cc_start: 0.8478 (pt) cc_final: 0.8139 (mp) REVERT: F 416 LYS cc_start: 0.7312 (pttt) cc_final: 0.6996 (pmtt) REVERT: E 12 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: E 131 ILE cc_start: 0.8479 (mt) cc_final: 0.8253 (mt) REVERT: E 151 ASP cc_start: 0.7100 (m-30) cc_final: 0.6855 (m-30) REVERT: E 250 ASP cc_start: 0.8414 (t0) cc_final: 0.8200 (t0) REVERT: E 342 ILE cc_start: 0.8483 (pt) cc_final: 0.8139 (mp) REVERT: E 358 LEU cc_start: 0.7876 (tp) cc_final: 0.7582 (tp) REVERT: E 416 LYS cc_start: 0.7400 (pttt) cc_final: 0.7032 (pmtt) outliers start: 16 outliers final: 12 residues processed: 136 average time/residue: 0.0973 time to fit residues: 19.3814 Evaluate side-chains 134 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 238 VAL 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 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 125 optimal weight: 0.0970 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.0270 chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 68 optimal weight: 3.9990 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4135 r_free = 0.4135 target = 0.198425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145088 restraints weight = 11347.011| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.35 r_work: 0.3511 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10938 Z= 0.102 Angle : 0.567 5.931 14866 Z= 0.291 Chirality : 0.043 0.148 1662 Planarity : 0.004 0.044 1874 Dihedral : 6.059 52.228 1736 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 1.27 % Allowed : 14.86 % Favored : 83.87 % 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: -2.69 (0.22), residues: 1260 helix: 1.04 (0.41), residues: 168 sheet: -1.73 (0.50), residues: 110 loop : -2.55 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 409 TYR 0.010 0.001 TYR F 507 PHE 0.015 0.001 PHE F 705 TRP 0.009 0.001 TRP F 251 HIS 0.003 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00236 (10884) covalent geometry : angle 0.55483 (14742) SS BOND : bond 0.00239 ( 38) SS BOND : angle 0.70150 ( 76) hydrogen bonds : bond 0.03444 ( 177) hydrogen bonds : angle 5.79652 ( 483) link_BETA1-4 : bond 0.00208 ( 2) link_BETA1-4 : angle 3.58101 ( 6) link_NAG-ASN : bond 0.00392 ( 14) link_NAG-ASN : angle 1.69907 ( 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 144 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: F 131 ILE cc_start: 0.8496 (mt) cc_final: 0.8257 (mt) REVERT: F 151 ASP cc_start: 0.7026 (m-30) cc_final: 0.6799 (m-30) REVERT: E 12 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: E 131 ILE cc_start: 0.8523 (mt) cc_final: 0.8309 (mt) REVERT: E 151 ASP cc_start: 0.7136 (m-30) cc_final: 0.6851 (m-30) REVERT: E 250 ASP cc_start: 0.8389 (t0) cc_final: 0.8167 (t0) REVERT: E 416 LYS cc_start: 0.7364 (pttt) cc_final: 0.7157 (pmtt) outliers start: 15 outliers final: 13 residues processed: 141 average time/residue: 0.0936 time to fit residues: 19.4282 Evaluate side-chains 135 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 132 ASP 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 489 TRP Chi-restraints excluded: chain F residue 531 VAL Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 238 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 0.0370 chunk 50 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 overall best weight: 1.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 108 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 = 0.4165 r_free = 0.4165 target = 0.199826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162475 restraints weight = 11361.008| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.48 r_work: 0.3446 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10938 Z= 0.190 Angle : 0.642 5.612 14866 Z= 0.331 Chirality : 0.046 0.146 1662 Planarity : 0.005 0.046 1874 Dihedral : 6.210 53.309 1736 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 2.20 % Allowed : 15.71 % 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: -2.78 (0.22), residues: 1260 helix: 0.90 (0.41), residues: 166 sheet: -1.85 (0.49), residues: 110 loop : -2.58 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 409 TYR 0.012 0.001 TYR E 60 PHE 0.018 0.002 PHE E 256 TRP 0.009 0.001 TRP F 251 HIS 0.004 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00470 (10884) covalent geometry : angle 0.63017 (14742) SS BOND : bond 0.00300 ( 38) SS BOND : angle 0.91551 ( 76) hydrogen bonds : bond 0.04193 ( 177) hydrogen bonds : angle 5.93953 ( 483) link_BETA1-4 : bond 0.00110 ( 2) link_BETA1-4 : angle 3.45848 ( 6) link_NAG-ASN : bond 0.00332 ( 14) link_NAG-ASN : angle 1.82913 ( 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 156 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: F 151 ASP cc_start: 0.7272 (m-30) cc_final: 0.7061 (m-30) REVERT: E 12 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: E 66 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8586 (p) REVERT: E 151 ASP cc_start: 0.7498 (m-30) cc_final: 0.7294 (m-30) REVERT: E 294 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6731 (tpt) outliers start: 26 outliers final: 18 residues processed: 149 average time/residue: 0.0821 time to fit residues: 18.6355 Evaluate side-chains 145 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 132 ASP Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 324 VAL 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 12 ASP Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 0.0010 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 108 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 = 0.4322 r_free = 0.4322 target = 0.215070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.185973 restraints weight = 11214.853| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.01 r_work: 0.3427 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10938 Z= 0.136 Angle : 0.617 7.286 14866 Z= 0.317 Chirality : 0.045 0.223 1662 Planarity : 0.004 0.041 1874 Dihedral : 6.185 54.100 1736 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.30 % Favored : 87.62 % Rotamer: Outliers : 2.87 % Allowed : 15.88 % Favored : 81.25 % 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: 1.10 (0.41), residues: 166 sheet: -1.77 (0.50), residues: 110 loop : -2.56 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 409 TYR 0.013 0.001 TYR F 507 PHE 0.017 0.001 PHE F 256 TRP 0.007 0.001 TRP F 251 HIS 0.004 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00334 (10884) covalent geometry : angle 0.60253 (14742) SS BOND : bond 0.00301 ( 38) SS BOND : angle 1.25873 ( 76) hydrogen bonds : bond 0.03818 ( 177) hydrogen bonds : angle 6.02679 ( 483) link_BETA1-4 : bond 0.00040 ( 2) link_BETA1-4 : angle 3.42184 ( 6) link_NAG-ASN : bond 0.00356 ( 14) link_NAG-ASN : angle 1.68951 ( 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 159 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.388 Fit side-chains REVERT: F 12 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: F 342 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8276 (mp) REVERT: F 533 ASP cc_start: 0.7585 (m-30) cc_final: 0.7254 (t0) REVERT: E 12 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: E 151 ASP cc_start: 0.7580 (m-30) cc_final: 0.7357 (m-30) REVERT: E 342 ILE cc_start: 0.8535 (pt) cc_final: 0.8188 (mp) outliers start: 34 outliers final: 21 residues processed: 149 average time/residue: 0.0878 time to fit residues: 19.4296 Evaluate side-chains 144 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 132 ASP 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 342 ILE Chi-restraints excluded: chain F residue 429 HIS 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 12 ASP 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 238 VAL Chi-restraints excluded: chain E residue 241 CYS Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 489 TRP Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain C residue 11 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 103 optimal weight: 0.0010 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4332 r_free = 0.4332 target = 0.216509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.194540 restraints weight = 11198.724| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.15 r_work: 0.3816 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2843 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= 0.113 Angle : 0.595 12.309 14866 Z= 0.303 Chirality : 0.044 0.163 1662 Planarity : 0.004 0.046 1874 Dihedral : 6.042 54.042 1736 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.90 % Favored : 88.02 % Rotamer: Outliers : 2.53 % Allowed : 16.30 % Favored : 81.17 % 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: -2.63 (0.22), residues: 1260 helix: 1.31 (0.42), residues: 166 sheet: -1.70 (0.51), residues: 110 loop : -2.54 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 409 TYR 0.012 0.001 TYR F 507 PHE 0.015 0.001 PHE E 705 TRP 0.010 0.001 TRP E 133 HIS 0.002 0.000 HIS F 280 Details of bonding type rmsd covalent geometry : bond 0.00272 (10884) covalent geometry : angle 0.58341 (14742) SS BOND : bond 0.00246 ( 38) SS BOND : angle 0.93012 ( 76) hydrogen bonds : bond 0.03441 ( 177) hydrogen bonds : angle 5.83338 ( 483) link_BETA1-4 : bond 0.00127 ( 2) link_BETA1-4 : angle 3.32675 ( 6) link_NAG-ASN : bond 0.00360 ( 14) link_NAG-ASN : angle 1.62158 ( 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 151 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: F 12 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: E 12 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7458 (m-30) REVERT: E 151 ASP cc_start: 0.7542 (m-30) cc_final: 0.7326 (m-30) REVERT: E 280 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7988 (t-90) REVERT: E 358 LEU cc_start: 0.8131 (tp) cc_final: 0.7839 (tp) outliers start: 30 outliers final: 23 residues processed: 141 average time/residue: 0.0889 time to fit residues: 18.6373 Evaluate side-chains 141 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 132 ASP 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 489 TRP Chi-restraints excluded: chain F residue 531 VAL 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 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 429 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 122 ASN F 429 HIS F 431 ASN E 122 ASN 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 = 0.4242 r_free = 0.4242 target = 0.206394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.180260 restraints weight = 11206.848| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.91 r_work: 0.3357 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10938 Z= 0.239 Angle : 0.744 12.984 14866 Z= 0.377 Chirality : 0.049 0.181 1662 Planarity : 0.005 0.049 1874 Dihedral : 6.565 56.255 1736 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.29 % Favored : 85.63 % Rotamer: Outliers : 2.96 % Allowed : 16.81 % Favored : 80.24 % 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: -2.82 (0.22), residues: 1260 helix: 0.96 (0.41), residues: 160 sheet: -1.67 (0.51), residues: 110 loop : -2.63 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 409 TYR 0.019 0.002 TYR E 60 PHE 0.022 0.002 PHE F 382 TRP 0.018 0.002 TRP F 183 HIS 0.009 0.001 HIS F 429 Details of bonding type rmsd covalent geometry : bond 0.00595 (10884) covalent geometry : angle 0.73103 (14742) SS BOND : bond 0.00308 ( 38) SS BOND : angle 1.23759 ( 76) hydrogen bonds : bond 0.04946 ( 177) hydrogen bonds : angle 6.22033 ( 483) link_BETA1-4 : bond 0.00394 ( 2) link_BETA1-4 : angle 3.27403 ( 6) link_NAG-ASN : bond 0.00324 ( 14) link_NAG-ASN : angle 1.99490 ( 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 161 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.421 Fit side-chains REVERT: F 12 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: F 342 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8448 (mp) REVERT: F 358 LEU cc_start: 0.8646 (tp) cc_final: 0.8367 (tp) REVERT: E 12 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: E 151 ASP cc_start: 0.7621 (m-30) cc_final: 0.7341 (m-30) REVERT: E 280 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.8120 (t-90) REVERT: E 342 ILE cc_start: 0.8710 (pt) cc_final: 0.8427 (mt) outliers start: 35 outliers final: 25 residues processed: 152 average time/residue: 0.0909 time to fit residues: 20.3871 Evaluate side-chains 147 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 CYS 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 132 ASP 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 342 ILE Chi-restraints excluded: chain F residue 429 HIS 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 12 ASP 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 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 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: 20.0000 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4330 r_free = 0.4330 target = 0.217483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.181993 restraints weight = 11236.278| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.34 r_work: 0.3623 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10938 Z= 0.144 Angle : 0.665 12.702 14866 Z= 0.336 Chirality : 0.046 0.193 1662 Planarity : 0.004 0.051 1874 Dihedral : 6.349 56.409 1736 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.22 % Favored : 87.70 % Rotamer: Outliers : 2.28 % Allowed : 17.23 % Favored : 80.49 % 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: 1.29 (0.42), residues: 160 sheet: -1.64 (0.53), residues: 110 loop : -2.60 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 409 TYR 0.016 0.001 TYR F 430 PHE 0.021 0.002 PHE F 428 TRP 0.012 0.002 TRP F 183 HIS 0.006 0.001 HIS F 429 Details of bonding type rmsd covalent geometry : bond 0.00353 (10884) covalent geometry : angle 0.65452 (14742) SS BOND : bond 0.00223 ( 38) SS BOND : angle 0.94065 ( 76) hydrogen bonds : bond 0.03924 ( 177) hydrogen bonds : angle 5.99480 ( 483) link_BETA1-4 : bond 0.00049 ( 2) link_BETA1-4 : angle 3.44822 ( 6) link_NAG-ASN : bond 0.00381 ( 14) link_NAG-ASN : angle 1.66108 ( 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 148 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.415 Fit side-chains REVERT: F 12 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: F 358 LEU cc_start: 0.8426 (tp) cc_final: 0.8165 (tp) REVERT: E 12 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: E 151 ASP cc_start: 0.7219 (m-30) cc_final: 0.6782 (m-30) REVERT: E 280 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8038 (t-90) REVERT: E 342 ILE cc_start: 0.8493 (pt) cc_final: 0.8220 (mp) outliers start: 27 outliers final: 23 residues processed: 139 average time/residue: 0.0887 time to fit residues: 18.4451 Evaluate side-chains 142 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 132 ASP 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 489 TRP Chi-restraints excluded: chain F residue 531 VAL 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 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 429 HIS 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 2 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 429 HIS ** 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 = 0.4310 r_free = 0.4310 target = 0.214058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.185241 restraints weight = 11127.567| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.76 r_work: 0.3683 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3359 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= 0.134 Angle : 0.638 12.288 14866 Z= 0.324 Chirality : 0.045 0.150 1662 Planarity : 0.004 0.053 1874 Dihedral : 6.264 56.572 1736 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.94 % Favored : 86.98 % Rotamer: Outliers : 2.28 % Allowed : 17.57 % 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: -2.67 (0.22), residues: 1260 helix: 1.42 (0.42), residues: 160 sheet: -1.49 (0.53), residues: 110 loop : -2.61 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 409 TYR 0.012 0.001 TYR E 507 PHE 0.018 0.001 PHE F 256 TRP 0.027 0.002 TRP F 183 HIS 0.005 0.001 HIS F 429 Details of bonding type rmsd covalent geometry : bond 0.00327 (10884) covalent geometry : angle 0.62751 (14742) SS BOND : bond 0.00220 ( 38) SS BOND : angle 0.88154 ( 76) hydrogen bonds : bond 0.03742 ( 177) hydrogen bonds : angle 5.91597 ( 483) link_BETA1-4 : bond 0.00041 ( 2) link_BETA1-4 : angle 3.26673 ( 6) link_NAG-ASN : bond 0.00344 ( 14) link_NAG-ASN : angle 1.65283 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.23 seconds wall clock time: 44 minutes 20.18 seconds (2660.18 seconds total)