Starting phenix.real_space_refine on Wed Feb 4 23:24:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mq3_48512/02_2026/9mq3_48512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mq3_48512/02_2026/9mq3_48512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mq3_48512/02_2026/9mq3_48512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mq3_48512/02_2026/9mq3_48512.map" model { file = "/net/cci-nas-00/data/ceres_data/9mq3_48512/02_2026/9mq3_48512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mq3_48512/02_2026/9mq3_48512.cif" } resolution = 3.22 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= 0.007 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 74 5.16 5 C 8532 2.51 5 N 2292 2.21 5 O 2627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13525 Number of models: 1 Model: "" Number of chains: 14 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 847 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2491 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 18, 'TRANS': 295} Chain breaks: 1 Chain: "b" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1341 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2491 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 18, 'TRANS': 295} Chain breaks: 1 Chain: "a" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1341 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2491 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 18, 'TRANS': 295} Chain breaks: 1 Chain: "c" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1341 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.73, per 1000 atoms: 0.20 Number of scatterers: 13525 At special positions: 0 Unit cell: (91.35, 105.85, 163.125, 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 74 16.00 O 2627 8.00 N 2292 7.00 C 8532 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.02 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS b 144 " - pdb=" SG CYS b 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS c 144 " - pdb=" SG CYS c 148 " distance=2.05 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 NAG-ASN " NAG A 401 " - " ASN A 169 " " NAG A 402 " - " ASN A 33 " " NAG A 403 " - " ASN A 289 " " NAG A 404 " - " ASN A 21 " " NAG B 401 " - " ASN B 169 " " NAG B 402 " - " ASN B 33 " " NAG B 403 " - " ASN B 21 " " NAG B 404 " - " ASN B 289 " " NAG C 401 " - " ASN C 169 " " NAG C 402 " - " ASN C 33 " " NAG C 403 " - " ASN C 21 " " NAG C 404 " - " ASN C 289 " " NAG a 301 " - " ASN a 154 " " NAG b 301 " - " ASN b 154 " " NAG c 301 " - " ASN c 154 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 624.0 milliseconds 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 22.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.596A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.880A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 27D through 30 removed outlier: 4.341A pdb=" N SER L 30 " --> pdb=" O SER L 27E" (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 65 through 71 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'b' and resid 37 through 59 Processing helix chain 'b' and resid 74 through 125 removed outlier: 3.575A pdb=" N ASP b 112 " --> pdb=" O LEU b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 155 Processing helix chain 'b' and resid 158 through 163 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'a' and resid 37 through 59 Processing helix chain 'a' and resid 74 through 127 Processing helix chain 'a' and resid 145 through 155 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.030A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'c' and resid 37 through 59 Processing helix chain 'c' and resid 74 through 125 removed outlier: 4.129A pdb=" N ASN c 104 " --> pdb=" O VAL c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 126 through 128 No H-bonds generated for 'chain 'c' and resid 126 through 128' Processing helix chain 'c' and resid 145 through 155 removed outlier: 3.800A pdb=" N ARG c 153 " --> pdb=" O MET c 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.602A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.283A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.442A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.074A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.389A pdb=" N ASP B 53 " --> pdb=" O THR B 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.487A pdb=" N LEU B 59 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AB2, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'B' and resid 151 through 153 removed outlier: 8.005A pdb=" N LEU B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 176 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AB5, first strand: chain 'b' and resid 130 through 132 removed outlier: 3.749A pdb=" N GLU b 139 " --> pdb=" O LYS b 131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.586A pdb=" N GLY A 16 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY a 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AB8, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB9, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.140A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 117 through 121 removed outlier: 7.218A pdb=" N HIS A 117 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 261 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 130 through 131 removed outlier: 3.720A pdb=" N ILE A 155 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'a' and resid 130 through 132 Processing sheet with id=AC5, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.810A pdb=" N CYS C 14 " --> pdb=" O HIS c 25 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 16 " --> pdb=" O GLY c 23 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY c 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 53 through 54 removed outlier: 5.593A pdb=" N ASP C 53 " --> pdb=" O THR C 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 102 removed outlier: 8.158A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 115 through 121 removed outlier: 6.536A pdb=" N ILE C 115 " --> pdb=" O LYS C 262A" (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS C 262A" --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N HIS C 117 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 261 " --> pdb=" O HIS C 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD2, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AD3, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.659A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AD5, first strand: chain 'c' and resid 130 through 132 434 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.51 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: 4366 1.34 - 1.47: 3421 1.47 - 1.59: 5948 1.59 - 1.71: 0 1.71 - 1.83: 108 Bond restraints: 13843 Sorted by residual: bond pdb=" C TYR c 159 " pdb=" N PRO c 160 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.39e+00 bond pdb=" CB CYS c 148 " pdb=" SG CYS c 148 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.99e+00 bond pdb=" CB ILE b 45 " pdb=" CG2 ILE b 45 " ideal model delta sigma weight residual 1.521 1.577 -0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" CB ILE b 55 " pdb=" CG2 ILE b 55 " ideal model delta sigma weight residual 1.521 1.570 -0.049 3.30e-02 9.18e+02 2.20e+00 ... (remaining 13838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 18232 2.35 - 4.70: 467 4.70 - 7.05: 61 7.05 - 9.40: 9 9.40 - 11.74: 1 Bond angle restraints: 18770 Sorted by residual: angle pdb=" C LEU A 320 " pdb=" N ARG A 321 " pdb=" CA ARG A 321 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" CA CYS c 144 " pdb=" CB CYS c 144 " pdb=" SG CYS c 144 " ideal model delta sigma weight residual 114.40 122.83 -8.43 2.30e+00 1.89e-01 1.34e+01 angle pdb=" CA GLN B 282 " pdb=" CB GLN B 282 " pdb=" CG GLN B 282 " ideal model delta sigma weight residual 114.10 121.24 -7.14 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CA LEU C 61 " pdb=" CB LEU C 61 " pdb=" CG LEU C 61 " ideal model delta sigma weight residual 116.30 128.04 -11.74 3.50e+00 8.16e-02 1.13e+01 angle pdb=" C CYS c 144 " pdb=" CA CYS c 144 " pdb=" CB CYS c 144 " ideal model delta sigma weight residual 109.38 115.61 -6.23 2.09e+00 2.29e-01 8.89e+00 ... (remaining 18765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 7785 17.39 - 34.78: 566 34.78 - 52.17: 72 52.17 - 69.56: 11 69.56 - 86.95: 7 Dihedral angle restraints: 8441 sinusoidal: 3596 harmonic: 4845 Sorted by residual: dihedral pdb=" CB CYS b 144 " pdb=" SG CYS b 144 " pdb=" SG CYS b 148 " pdb=" CB CYS b 148 " ideal model delta sinusoidal sigma weight residual 93.00 144.80 -51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS a 144 " pdb=" SG CYS a 144 " pdb=" SG CYS a 148 " pdb=" CB CYS a 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.31 -50.31 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.35 -41.35 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 8438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1581 0.054 - 0.108: 354 0.108 - 0.161: 111 0.161 - 0.215: 3 0.215 - 0.269: 4 Chirality restraints: 2053 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 289 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE B 288 " pdb=" CA ILE B 288 " pdb=" CG1 ILE B 288 " pdb=" CG2 ILE B 288 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C1 NAG C 403 " pdb=" ND2 ASN C 21 " pdb=" C2 NAG C 403 " pdb=" O5 NAG C 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2050 not shown) Planarity restraints: 2433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN c 28 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" CG ASN c 28 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN c 28 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN c 28 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 161 " 0.048 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO C 162 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 7 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO L 8 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.034 5.00e-02 4.00e+02 ... (remaining 2430 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 184 2.64 - 3.21: 12604 3.21 - 3.77: 20376 3.77 - 4.34: 29584 4.34 - 4.90: 49072 Nonbonded interactions: 111820 Sorted by model distance: nonbonded pdb=" O LEU B 70 " pdb=" OH TYR B 258 " model vdw 2.076 3.040 nonbonded pdb=" OG SER C 113 " pdb=" O SER C 265 " model vdw 2.099 3.040 nonbonded pdb=" O VAL C 309 " pdb=" OG1 THR c 93 " model vdw 2.132 3.040 nonbonded pdb=" OG SER A 185 " pdb=" OE1 GLN A 191 " model vdw 2.133 3.040 nonbonded pdb=" OG SER B 101 " pdb=" OD1 ASP B 231 " model vdw 2.160 3.040 ... (remaining 111815 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 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 9.110 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.130 Find NCS groups from input model: 0.200 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.068 13873 Z= 0.225 Angle : 0.900 11.745 18845 Z= 0.462 Chirality : 0.052 0.269 2053 Planarity : 0.006 0.072 2418 Dihedral : 11.888 86.949 5300 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.19), residues: 1651 helix: -0.68 (0.25), residues: 366 sheet: -2.35 (0.30), residues: 245 loop : -2.07 (0.17), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 127 TYR 0.023 0.002 TYR A 105 PHE 0.024 0.003 PHE b 3 TRP 0.025 0.002 TRP B 153 HIS 0.010 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00533 (13843) covalent geometry : angle 0.88997 (18770) SS BOND : bond 0.00649 ( 15) SS BOND : angle 2.38298 ( 30) hydrogen bonds : bond 0.15146 ( 434) hydrogen bonds : angle 7.60884 ( 1182) link_NAG-ASN : bond 0.00497 ( 15) link_NAG-ASN : angle 2.19864 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 THR cc_start: 0.8842 (p) cc_final: 0.8324 (t) REVERT: a 37 ASP cc_start: 0.6497 (t0) cc_final: 0.6181 (m-30) REVERT: a 159 TYR cc_start: 0.6245 (t80) cc_final: 0.5975 (t80) REVERT: C 165 LYS cc_start: 0.6527 (mttt) cc_final: 0.6233 (mttt) REVERT: C 196 LYS cc_start: 0.7421 (tmtt) cc_final: 0.6969 (ttpt) REVERT: C 274 TYR cc_start: 0.7061 (t80) cc_final: 0.6678 (t80) REVERT: c 86 ASP cc_start: 0.7682 (m-30) cc_final: 0.7403 (m-30) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.1450 time to fit residues: 93.1729 Evaluate side-chains 303 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0000 chunk 149 optimal weight: 6.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN B 150 ASN b 60 ASN ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 HIS A 186 ASN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 125 GLN a 129 ASN C 18 HIS c 114 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.161280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.141610 restraints weight = 21544.308| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.48 r_work: 0.3701 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13873 Z= 0.221 Angle : 0.707 9.944 18845 Z= 0.361 Chirality : 0.049 0.250 2053 Planarity : 0.005 0.063 2418 Dihedral : 6.449 59.242 2125 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.64 % Allowed : 11.05 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.18), residues: 1651 helix: -0.66 (0.25), residues: 372 sheet: -1.88 (0.32), residues: 234 loop : -1.95 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 149 TYR 0.024 0.002 TYR C 105 PHE 0.020 0.002 PHE a 9 TRP 0.024 0.002 TRP B 153 HIS 0.006 0.001 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00491 (13843) covalent geometry : angle 0.69671 (18770) SS BOND : bond 0.00943 ( 15) SS BOND : angle 1.62859 ( 30) hydrogen bonds : bond 0.05774 ( 434) hydrogen bonds : angle 6.47479 ( 1182) link_NAG-ASN : bond 0.00322 ( 15) link_NAG-ASN : angle 2.19432 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.8643 (m-80) cc_final: 0.8327 (m-80) REVERT: B 32 LYS cc_start: 0.7576 (mmtp) cc_final: 0.7087 (mmtt) REVERT: B 41 ASP cc_start: 0.8203 (p0) cc_final: 0.7923 (p0) REVERT: b 25 HIS cc_start: 0.7731 (t70) cc_final: 0.7240 (t70) REVERT: b 38 LYS cc_start: 0.4811 (tttt) cc_final: 0.4566 (tttt) REVERT: b 55 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8435 (mp) REVERT: b 161 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7918 (tm-30) REVERT: A 121 ILE cc_start: 0.8813 (pt) cc_final: 0.8596 (pt) REVERT: A 292 MET cc_start: 0.8512 (mmt) cc_final: 0.8256 (mmt) REVERT: C 32 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8299 (mptt) REVERT: C 230 MET cc_start: 0.7946 (mtt) cc_final: 0.7644 (mtt) REVERT: C 274 TYR cc_start: 0.6963 (t80) cc_final: 0.6696 (t80) REVERT: c 39 GLU cc_start: 0.7220 (pt0) cc_final: 0.6994 (pt0) REVERT: c 59 MET cc_start: 0.8250 (mmm) cc_final: 0.7809 (mmm) REVERT: c 62 GLN cc_start: 0.7377 (mp10) cc_final: 0.6667 (mp10) REVERT: c 131 LYS cc_start: 0.7429 (tptt) cc_final: 0.6953 (tttm) outliers start: 24 outliers final: 15 residues processed: 318 average time/residue: 0.1437 time to fit residues: 62.3347 Evaluate side-chains 279 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 163 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 161 optimal weight: 0.1980 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN L 45 GLN B 222 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.160971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.141033 restraints weight = 21492.319| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.48 r_work: 0.3698 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13873 Z= 0.163 Angle : 0.619 9.525 18845 Z= 0.318 Chirality : 0.046 0.257 2053 Planarity : 0.005 0.057 2418 Dihedral : 6.249 59.803 2125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.05 % Allowed : 12.62 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.24 (0.19), residues: 1651 helix: -0.53 (0.26), residues: 375 sheet: -1.76 (0.31), residues: 262 loop : -1.84 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 123 TYR 0.019 0.002 TYR H 52 PHE 0.027 0.002 PHE B 118 TRP 0.017 0.001 TRP B 153 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00359 (13843) covalent geometry : angle 0.60980 (18770) SS BOND : bond 0.00440 ( 15) SS BOND : angle 1.27398 ( 30) hydrogen bonds : bond 0.05372 ( 434) hydrogen bonds : angle 6.25850 ( 1182) link_NAG-ASN : bond 0.00233 ( 15) link_NAG-ASN : angle 2.10138 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 THR cc_start: 0.6850 (t) cc_final: 0.6605 (p) REVERT: L 87 TYR cc_start: 0.8599 (m-80) cc_final: 0.8225 (m-80) REVERT: B 32 LYS cc_start: 0.7547 (mmtp) cc_final: 0.7303 (mmtm) REVERT: B 41 ASP cc_start: 0.8354 (p0) cc_final: 0.8033 (p0) REVERT: B 268 MET cc_start: 0.7317 (mtm) cc_final: 0.6899 (mtt) REVERT: B 314 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8769 (mp) REVERT: b 25 HIS cc_start: 0.7822 (t70) cc_final: 0.7411 (t70) REVERT: b 38 LYS cc_start: 0.4793 (tptt) cc_final: 0.4561 (tptt) REVERT: b 161 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7943 (tm-30) REVERT: A 292 MET cc_start: 0.8528 (mmt) cc_final: 0.8284 (mmt) REVERT: a 150 GLU cc_start: 0.7393 (pt0) cc_final: 0.7033 (tt0) REVERT: C 32 LYS cc_start: 0.8767 (mmtm) cc_final: 0.8362 (mptt) REVERT: C 207 SER cc_start: 0.7232 (m) cc_final: 0.6991 (t) REVERT: C 274 TYR cc_start: 0.6940 (t80) cc_final: 0.6688 (t80) REVERT: c 89 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8142 (tp) REVERT: c 131 LYS cc_start: 0.7398 (tptt) cc_final: 0.6938 (tttm) outliers start: 30 outliers final: 15 residues processed: 314 average time/residue: 0.1504 time to fit residues: 64.5021 Evaluate side-chains 287 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 270 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 46 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN c 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137989 restraints weight = 21653.258| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.50 r_work: 0.3647 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13873 Z= 0.201 Angle : 0.642 9.515 18845 Z= 0.328 Chirality : 0.046 0.250 2053 Planarity : 0.005 0.057 2418 Dihedral : 6.323 59.222 2125 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.46 % Allowed : 14.32 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.19), residues: 1651 helix: -0.48 (0.26), residues: 372 sheet: -1.38 (0.34), residues: 232 loop : -1.83 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 123 TYR 0.024 0.002 TYR H 50 PHE 0.032 0.002 PHE B 118 TRP 0.020 0.001 TRP B 153 HIS 0.006 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00451 (13843) covalent geometry : angle 0.63364 (18770) SS BOND : bond 0.00508 ( 15) SS BOND : angle 1.14781 ( 30) hydrogen bonds : bond 0.05393 ( 434) hydrogen bonds : angle 6.24532 ( 1182) link_NAG-ASN : bond 0.00254 ( 15) link_NAG-ASN : angle 2.06320 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 MET cc_start: 0.7980 (mmt) cc_final: 0.7685 (mmt) REVERT: L 87 TYR cc_start: 0.8645 (m-80) cc_final: 0.8276 (m-80) REVERT: B 32 LYS cc_start: 0.7616 (mmtp) cc_final: 0.7340 (mmtm) REVERT: B 41 ASP cc_start: 0.8692 (p0) cc_final: 0.8468 (p0) REVERT: B 268 MET cc_start: 0.7300 (mtm) cc_final: 0.7042 (mtt) REVERT: B 314 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8785 (mp) REVERT: b 25 HIS cc_start: 0.7931 (t70) cc_final: 0.7490 (t70) REVERT: A 259 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8012 (ttpp) REVERT: a 150 GLU cc_start: 0.7471 (pt0) cc_final: 0.7051 (tt0) REVERT: C 30 MET cc_start: 0.8635 (mtt) cc_final: 0.8409 (ttm) REVERT: C 274 TYR cc_start: 0.6964 (t80) cc_final: 0.6738 (t80) REVERT: c 62 GLN cc_start: 0.7092 (mp10) cc_final: 0.6437 (mp10) REVERT: c 131 LYS cc_start: 0.7464 (tptt) cc_final: 0.7040 (tttm) outliers start: 36 outliers final: 20 residues processed: 306 average time/residue: 0.1548 time to fit residues: 64.8304 Evaluate side-chains 285 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100DASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN ** b 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN a 79 ASN C 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.154948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135037 restraints weight = 21805.229| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.45 r_work: 0.3612 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13873 Z= 0.270 Angle : 0.722 9.503 18845 Z= 0.369 Chirality : 0.049 0.237 2053 Planarity : 0.005 0.061 2418 Dihedral : 6.616 59.776 2125 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.73 % Allowed : 15.83 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.21 (0.19), residues: 1651 helix: -0.58 (0.25), residues: 372 sheet: -1.47 (0.33), residues: 242 loop : -1.88 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 173 TYR 0.034 0.002 TYR H 50 PHE 0.030 0.002 PHE B 118 TRP 0.020 0.002 TRP B 153 HIS 0.008 0.002 HIS a 25 Details of bonding type rmsd covalent geometry : bond 0.00613 (13843) covalent geometry : angle 0.71268 (18770) SS BOND : bond 0.00616 ( 15) SS BOND : angle 1.61231 ( 30) hydrogen bonds : bond 0.05729 ( 434) hydrogen bonds : angle 6.42771 ( 1182) link_NAG-ASN : bond 0.00311 ( 15) link_NAG-ASN : angle 2.10852 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.8717 (m-80) cc_final: 0.8307 (m-80) REVERT: L 103 LYS cc_start: 0.8306 (tttm) cc_final: 0.8050 (ttpt) REVERT: B 32 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7326 (mmtm) REVERT: B 268 MET cc_start: 0.7449 (mtm) cc_final: 0.7240 (mtt) REVERT: B 314 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8825 (mp) REVERT: b 25 HIS cc_start: 0.8110 (t70) cc_final: 0.7592 (t70) REVERT: A 60 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 107 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6994 (mm-30) REVERT: A 259 LYS cc_start: 0.8438 (ttmt) cc_final: 0.8029 (ttpp) REVERT: a 102 MET cc_start: 0.8071 (mtp) cc_final: 0.7606 (mtp) REVERT: C 32 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8296 (mptt) REVERT: C 37 THR cc_start: 0.7956 (OUTLIER) cc_final: 0.7579 (p) REVERT: C 274 TYR cc_start: 0.7053 (t80) cc_final: 0.6835 (t80) outliers start: 40 outliers final: 29 residues processed: 313 average time/residue: 0.1523 time to fit residues: 65.4956 Evaluate side-chains 297 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain b residue 22 TYR Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 8 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 140 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 137 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 HIS ** b 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 HIS a 30 GLN C 18 HIS C 47 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138259 restraints weight = 21522.080| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.50 r_work: 0.3652 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13873 Z= 0.143 Angle : 0.614 9.405 18845 Z= 0.314 Chirality : 0.045 0.250 2053 Planarity : 0.004 0.055 2418 Dihedral : 6.219 57.606 2125 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.32 % Allowed : 16.92 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.10 (0.19), residues: 1651 helix: -0.38 (0.26), residues: 372 sheet: -1.58 (0.30), residues: 287 loop : -1.79 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 123 TYR 0.022 0.002 TYR H 50 PHE 0.014 0.002 PHE B 118 TRP 0.012 0.001 TRP B 153 HIS 0.007 0.001 HIS a 25 Details of bonding type rmsd covalent geometry : bond 0.00317 (13843) covalent geometry : angle 0.60556 (18770) SS BOND : bond 0.00408 ( 15) SS BOND : angle 1.28485 ( 30) hydrogen bonds : bond 0.05053 ( 434) hydrogen bonds : angle 6.20504 ( 1182) link_NAG-ASN : bond 0.00243 ( 15) link_NAG-ASN : angle 1.96085 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.8640 (m-80) cc_final: 0.8179 (m-80) REVERT: B 31 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6347 (tp30) REVERT: B 32 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7227 (mmtm) REVERT: B 90 ARG cc_start: 0.6112 (ttm110) cc_final: 0.5593 (mtt-85) REVERT: B 314 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8776 (mp) REVERT: A 259 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7952 (ttpp) REVERT: a 6 ILE cc_start: 0.6873 (pt) cc_final: 0.6435 (mt) REVERT: a 102 MET cc_start: 0.8030 (mtp) cc_final: 0.7575 (mtp) REVERT: a 150 GLU cc_start: 0.7524 (pt0) cc_final: 0.7253 (tt0) REVERT: C 32 LYS cc_start: 0.8791 (mmtp) cc_final: 0.8121 (mptt) REVERT: C 37 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7576 (p) REVERT: C 274 TYR cc_start: 0.7030 (t80) cc_final: 0.6805 (t80) REVERT: c 62 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.5378 (mp10) REVERT: c 127 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7672 (mtm-85) outliers start: 34 outliers final: 21 residues processed: 309 average time/residue: 0.1536 time to fit residues: 65.1891 Evaluate side-chains 293 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain b residue 22 TYR Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN C 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.157787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137985 restraints weight = 21510.954| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.47 r_work: 0.3647 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13873 Z= 0.167 Angle : 0.632 9.477 18845 Z= 0.323 Chirality : 0.046 0.251 2053 Planarity : 0.005 0.087 2418 Dihedral : 6.166 57.128 2125 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.86 % Allowed : 17.12 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.00 (0.19), residues: 1651 helix: -0.29 (0.26), residues: 369 sheet: -1.50 (0.31), residues: 277 loop : -1.73 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 173 TYR 0.021 0.002 TYR H 50 PHE 0.020 0.002 PHE A 118 TRP 0.011 0.001 TRP B 153 HIS 0.009 0.001 HIS a 25 Details of bonding type rmsd covalent geometry : bond 0.00377 (13843) covalent geometry : angle 0.62471 (18770) SS BOND : bond 0.00363 ( 15) SS BOND : angle 1.17109 ( 30) hydrogen bonds : bond 0.05043 ( 434) hydrogen bonds : angle 6.16159 ( 1182) link_NAG-ASN : bond 0.00226 ( 15) link_NAG-ASN : angle 1.92007 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.8666 (m-80) cc_final: 0.8221 (m-80) REVERT: B 31 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6405 (tp30) REVERT: B 90 ARG cc_start: 0.6154 (ttm110) cc_final: 0.5672 (mtt-85) REVERT: B 314 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8792 (mp) REVERT: A 259 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7926 (ttpp) REVERT: a 6 ILE cc_start: 0.6891 (pt) cc_final: 0.6517 (mt) REVERT: a 86 ASP cc_start: 0.7608 (t0) cc_final: 0.7261 (t0) REVERT: a 150 GLU cc_start: 0.7573 (pt0) cc_final: 0.7310 (tt0) REVERT: C 32 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8187 (mptt) REVERT: C 37 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (p) REVERT: C 274 TYR cc_start: 0.7040 (t80) cc_final: 0.6821 (t80) REVERT: c 59 MET cc_start: 0.7950 (mmm) cc_final: 0.7083 (mmm) REVERT: c 62 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.5336 (mp10) REVERT: c 89 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7919 (tt) REVERT: c 127 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7658 (mtm-85) outliers start: 42 outliers final: 25 residues processed: 303 average time/residue: 0.1356 time to fit residues: 57.0435 Evaluate side-chains 287 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain b residue 22 TYR Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 162 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100DASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN A 186 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.156233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136259 restraints weight = 21499.035| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.48 r_work: 0.3619 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13873 Z= 0.196 Angle : 0.653 9.495 18845 Z= 0.333 Chirality : 0.046 0.245 2053 Planarity : 0.005 0.056 2418 Dihedral : 6.230 57.297 2125 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.73 % Allowed : 16.92 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.19), residues: 1651 helix: -0.31 (0.26), residues: 369 sheet: -1.49 (0.29), residues: 317 loop : -1.78 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 173 TYR 0.025 0.002 TYR H 50 PHE 0.013 0.002 PHE b 110 TRP 0.013 0.001 TRP C 153 HIS 0.007 0.001 HIS b 111 Details of bonding type rmsd covalent geometry : bond 0.00445 (13843) covalent geometry : angle 0.64591 (18770) SS BOND : bond 0.00407 ( 15) SS BOND : angle 1.21532 ( 30) hydrogen bonds : bond 0.05167 ( 434) hydrogen bonds : angle 6.22338 ( 1182) link_NAG-ASN : bond 0.00235 ( 15) link_NAG-ASN : angle 1.91703 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 270 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.8694 (m-80) cc_final: 0.8273 (m-80) REVERT: B 31 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6430 (tp30) REVERT: B 90 ARG cc_start: 0.6164 (ttm110) cc_final: 0.5696 (mtt-85) REVERT: B 314 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 259 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7989 (ttpp) REVERT: a 6 ILE cc_start: 0.6958 (pt) cc_final: 0.6590 (mt) REVERT: a 86 ASP cc_start: 0.7632 (t0) cc_final: 0.7296 (t0) REVERT: a 102 MET cc_start: 0.8162 (mtp) cc_final: 0.7853 (mtp) REVERT: a 150 GLU cc_start: 0.7570 (pt0) cc_final: 0.7263 (tt0) REVERT: C 32 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8195 (mptt) REVERT: C 37 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7538 (p) REVERT: c 62 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5358 (mp10) REVERT: c 89 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7938 (tt) outliers start: 40 outliers final: 32 residues processed: 295 average time/residue: 0.1440 time to fit residues: 58.7479 Evaluate side-chains 299 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain b residue 22 TYR Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100DASN L 70 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133525 restraints weight = 21719.865| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.48 r_work: 0.3580 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13873 Z= 0.254 Angle : 0.712 9.548 18845 Z= 0.365 Chirality : 0.048 0.242 2053 Planarity : 0.005 0.058 2418 Dihedral : 6.431 58.244 2125 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.80 % Allowed : 17.80 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.19), residues: 1651 helix: -0.42 (0.26), residues: 369 sheet: -1.46 (0.31), residues: 287 loop : -1.86 (0.18), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 54 TYR 0.030 0.002 TYR H 50 PHE 0.017 0.002 PHE b 110 TRP 0.017 0.002 TRP C 153 HIS 0.006 0.001 HIS b 111 Details of bonding type rmsd covalent geometry : bond 0.00578 (13843) covalent geometry : angle 0.70471 (18770) SS BOND : bond 0.00502 ( 15) SS BOND : angle 1.31614 ( 30) hydrogen bonds : bond 0.05456 ( 434) hydrogen bonds : angle 6.40013 ( 1182) link_NAG-ASN : bond 0.00287 ( 15) link_NAG-ASN : angle 2.01495 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 87 TYR cc_start: 0.8732 (m-80) cc_final: 0.8318 (m-80) REVERT: L 103 LYS cc_start: 0.8405 (tttm) cc_final: 0.8101 (ttpt) REVERT: B 31 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6428 (tp30) REVERT: B 90 ARG cc_start: 0.6262 (ttm110) cc_final: 0.5790 (mtt-85) REVERT: B 307 LYS cc_start: 0.6672 (mmmt) cc_final: 0.6238 (mmtm) REVERT: B 314 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8855 (mp) REVERT: B 320 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6377 (mp) REVERT: A 259 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8041 (ttpp) REVERT: a 6 ILE cc_start: 0.7069 (pt) cc_final: 0.6681 (mt) REVERT: a 86 ASP cc_start: 0.7688 (t0) cc_final: 0.7374 (t0) REVERT: a 102 MET cc_start: 0.8189 (mtp) cc_final: 0.7796 (mtp) REVERT: a 150 GLU cc_start: 0.7604 (pt0) cc_final: 0.7265 (tt0) REVERT: C 32 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8210 (mptt) REVERT: C 37 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7493 (p) REVERT: c 62 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.5337 (mp10) REVERT: c 89 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7948 (tt) outliers start: 41 outliers final: 32 residues processed: 296 average time/residue: 0.1515 time to fit residues: 62.1066 Evaluate side-chains 298 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain b residue 22 TYR Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 19 ASP Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 76 ARG Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 12 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.158715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138753 restraints weight = 21622.418| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.51 r_work: 0.3651 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13873 Z= 0.150 Angle : 0.634 9.509 18845 Z= 0.327 Chirality : 0.046 0.252 2053 Planarity : 0.004 0.056 2418 Dihedral : 6.152 56.816 2125 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.11 % Allowed : 18.69 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.19), residues: 1651 helix: -0.15 (0.26), residues: 351 sheet: -1.46 (0.30), residues: 307 loop : -1.70 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 123 TYR 0.019 0.002 TYR H 50 PHE 0.012 0.002 PHE a 9 TRP 0.012 0.001 TRP C 153 HIS 0.005 0.001 HIS b 111 Details of bonding type rmsd covalent geometry : bond 0.00336 (13843) covalent geometry : angle 0.62630 (18770) SS BOND : bond 0.00316 ( 15) SS BOND : angle 1.17047 ( 30) hydrogen bonds : bond 0.04969 ( 434) hydrogen bonds : angle 6.22066 ( 1182) link_NAG-ASN : bond 0.00222 ( 15) link_NAG-ASN : angle 1.89239 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3302 Ramachandran restraints generated. 1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 77 ARG cc_start: 0.7379 (mmp80) cc_final: 0.6878 (mtt90) REVERT: L 87 TYR cc_start: 0.8654 (m-80) cc_final: 0.8212 (m-80) REVERT: B 31 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6399 (tp30) REVERT: B 90 ARG cc_start: 0.6106 (ttm110) cc_final: 0.5776 (mtt-85) REVERT: B 314 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8808 (mp) REVERT: B 316 LEU cc_start: 0.8565 (tt) cc_final: 0.8312 (mt) REVERT: A 259 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7957 (ttpp) REVERT: a 6 ILE cc_start: 0.6841 (pt) cc_final: 0.6637 (mt) REVERT: a 86 ASP cc_start: 0.7587 (t0) cc_final: 0.7254 (t0) REVERT: a 102 MET cc_start: 0.8054 (mtp) cc_final: 0.7759 (mtp) REVERT: a 150 GLU cc_start: 0.7586 (pt0) cc_final: 0.7274 (tt0) REVERT: C 32 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8203 (mptt) REVERT: c 59 MET cc_start: 0.7843 (mmm) cc_final: 0.6987 (mmm) REVERT: c 62 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.5224 (mp10) REVERT: c 89 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7849 (tt) outliers start: 31 outliers final: 23 residues processed: 293 average time/residue: 0.1510 time to fit residues: 61.1435 Evaluate side-chains 285 residues out of total 1466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 258 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain b residue 22 TYR Chi-restraints excluded: chain b residue 126 LEU Chi-restraints excluded: chain b residue 135 ASN Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 195 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain a residue 162 TYR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain c residue 22 TYR Chi-restraints excluded: chain c residue 62 GLN Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 148 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137947 restraints weight = 21809.700| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.52 r_work: 0.3637 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13873 Z= 0.171 Angle : 0.653 9.501 18845 Z= 0.336 Chirality : 0.046 0.247 2053 Planarity : 0.005 0.058 2418 Dihedral : 6.166 56.656 2125 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.05 % Allowed : 18.83 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.90 (0.19), residues: 1651 helix: -0.13 (0.26), residues: 351 sheet: -1.37 (0.30), residues: 307 loop : -1.69 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.022 0.002 TYR H 50 PHE 0.033 0.002 PHE A 147 TRP 0.013 0.001 TRP C 153 HIS 0.019 0.001 HIS b 26 Details of bonding type rmsd covalent geometry : bond 0.00386 (13843) covalent geometry : angle 0.64604 (18770) SS BOND : bond 0.00351 ( 15) SS BOND : angle 1.20276 ( 30) hydrogen bonds : bond 0.05013 ( 434) hydrogen bonds : angle 6.22200 ( 1182) link_NAG-ASN : bond 0.00245 ( 15) link_NAG-ASN : angle 1.84987 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3342.72 seconds wall clock time: 58 minutes 31.48 seconds (3511.48 seconds total)