Starting phenix.real_space_refine on Wed Mar 4 01:10:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n8j_49130/03_2026/9n8j_49130.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n8j_49130/03_2026/9n8j_49130.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 { model { file = "/net/cci-nas-00/data/ceres_data/9n8j_49130/03_2026/9n8j_49130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n8j_49130/03_2026/9n8j_49130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n8j_49130/03_2026/9n8j_49130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n8j_49130/03_2026/9n8j_49130.map" } 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= 0.025 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 40 5.16 5 C 6022 2.51 5 N 1569 2.21 5 O 1881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9512 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "C" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 966 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "G" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 839 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "I" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 834 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "X" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2436 Classifications: {'peptide': 308} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 14, 'TRANS': 289} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.23, per 1000 atoms: 0.23 Number of scatterers: 9512 At special positions: 0 Unit cell: (76.26, 133.92, 140.43, 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 40 16.00 O 1881 8.00 N 1569 7.00 C 6022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 42 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 75 " - pdb=" SG CYS X 155 " distance=2.03 Simple disulfide: pdb=" SG CYS X 185 " - pdb=" SG CYS X 214 " distance=2.03 Simple disulfide: pdb=" SG CYS X 231 " - pdb=" SG CYS X 299 " distance=2.03 Simple disulfide: pdb=" SG CYS X 239 " - pdb=" SG CYS X 297 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-6 " NAG A 1 " - " FUC A 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN D 54 " Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 362.6 milliseconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 28 sheets defined 7.3% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.886A pdb=" N SER B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 52A through 55 removed outlier: 3.762A pdb=" N THR B 55 " --> pdb=" O SER B 52A" (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52A through 55' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.600A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 65 removed outlier: 4.407A pdb=" N SER D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 4.219A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.672A pdb=" N LYS F 64 " --> pdb=" O ASP F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 27B through 31 removed outlier: 3.675A pdb=" N ASN G 31 " --> pdb=" O ILE G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.683A pdb=" N GLU G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 55 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 28 Processing helix chain 'X' and resid 112 through 116 Processing helix chain 'X' and resid 131 through 134 Processing helix chain 'X' and resid 202 through 206 Processing helix chain 'X' and resid 259 through 264 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.120A pdb=" N GLY B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.976A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.584A pdb=" N TRP D 35A" --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP D 36 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 100C through 100F removed outlier: 6.952A pdb=" N ILE X 212 " --> pdb=" O TYR X 307 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR X 309 " --> pdb=" O ILE X 212 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS X 214 " --> pdb=" O THR X 309 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N THR X 311 " --> pdb=" O CYS X 214 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL X 216 " --> pdb=" O THR X 311 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.542A pdb=" N ALA E 13 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.542A pdb=" N ALA E 13 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.743A pdb=" N LEU F 18 " --> pdb=" O MET F 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET F 82 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 81 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.468A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.468A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.875A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.875A pdb=" N VAL G 11 " --> pdb=" O THR G 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.035A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.234A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.234A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'X' and resid 29 through 32 removed outlier: 6.479A pdb=" N ASP X 29 " --> pdb=" O LYS X 59 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU X 61 " --> pdb=" O ASP X 29 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR X 31 " --> pdb=" O GLU X 61 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LYS X 63 " --> pdb=" O TYR X 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 39 through 43 removed outlier: 6.088A pdb=" N TYR X 40 " --> pdb=" O LYS X 72 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE X 74 " --> pdb=" O TYR X 40 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N CYS X 42 " --> pdb=" O ILE X 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 98 through 103 Processing sheet with id=AC8, first strand: chain 'X' and resid 124 through 125 Processing sheet with id=AC9, first strand: chain 'X' and resid 196 through 200 removed outlier: 6.874A pdb=" N GLY X 184 " --> pdb=" O SER X 198 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER X 200 " --> pdb=" O GLY X 184 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN X 186 " --> pdb=" O SER X 200 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LYS X 181 " --> pdb=" O TRP X 226 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLY X 228 " --> pdb=" O LYS X 181 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS X 183 " --> pdb=" O GLY X 228 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N ASN X 230 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N CYS X 185 " --> pdb=" O ASN X 230 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 242 through 244 367 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.04 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: 3000 1.34 - 1.46: 2393 1.46 - 1.58: 4285 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 9732 Sorted by residual: bond pdb=" CA PRO D 40 " pdb=" C PRO D 40 " ideal model delta sigma weight residual 1.514 1.495 0.019 5.50e-03 3.31e+04 1.20e+01 bond pdb=" C ASN X 230 " pdb=" N CYS X 231 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.44e-02 4.82e+03 2.08e+00 bond pdb=" N VAL X 289 " pdb=" CA VAL X 289 " ideal model delta sigma weight residual 1.465 1.452 0.012 1.02e-02 9.61e+03 1.48e+00 bond pdb=" C VAL F 12 " pdb=" N GLN F 13 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.47e-02 4.63e+03 1.23e+00 bond pdb=" CB PHE H 53 " pdb=" CG PHE H 53 " ideal model delta sigma weight residual 1.502 1.526 -0.024 2.30e-02 1.89e+03 1.13e+00 ... (remaining 9727 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 13034 2.28 - 4.56: 159 4.56 - 6.84: 11 6.84 - 9.12: 2 9.12 - 11.40: 1 Bond angle restraints: 13207 Sorted by residual: angle pdb=" CA LEU D 82 " pdb=" CB LEU D 82 " pdb=" CG LEU D 82 " ideal model delta sigma weight residual 116.30 127.70 -11.40 3.50e+00 8.16e-02 1.06e+01 angle pdb=" C ASN F 52A" pdb=" CA ASN F 52A" pdb=" CB ASN F 52A" ideal model delta sigma weight residual 110.42 116.82 -6.40 1.99e+00 2.53e-01 1.03e+01 angle pdb=" C ASP C 50 " pdb=" N ALA C 51 " pdb=" CA ALA C 51 " ideal model delta sigma weight residual 121.54 127.53 -5.99 1.91e+00 2.74e-01 9.84e+00 angle pdb=" N SER G 65 " pdb=" CA SER G 65 " pdb=" C SER G 65 " ideal model delta sigma weight residual 107.88 111.89 -4.01 1.41e+00 5.03e-01 8.07e+00 angle pdb=" N GLY E 68 " pdb=" CA GLY E 68 " pdb=" C GLY E 68 " ideal model delta sigma weight residual 112.83 116.14 -3.31 1.22e+00 6.72e-01 7.36e+00 ... (remaining 13202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 5513 15.98 - 31.97: 227 31.97 - 47.95: 67 47.95 - 63.93: 28 63.93 - 79.91: 9 Dihedral angle restraints: 5844 sinusoidal: 2312 harmonic: 3532 Sorted by residual: dihedral pdb=" CA ALA D 85 " pdb=" C ALA D 85 " pdb=" N ASP D 86 " pdb=" CA ASP D 86 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA TYR X 152 " pdb=" C TYR X 152 " pdb=" N PHE X 153 " pdb=" CA PHE X 153 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP X 224 " pdb=" C ASP X 224 " pdb=" N VAL X 225 " pdb=" CA VAL X 225 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 899 0.031 - 0.062: 365 0.062 - 0.093: 86 0.093 - 0.125: 96 0.125 - 0.156: 15 Chirality restraints: 1461 Sorted by residual: chirality pdb=" C1 FUC A 2 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 2 " pdb=" O5 FUC A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 7.89e-01 chirality pdb=" CA ILE X 236 " pdb=" N ILE X 236 " pdb=" C ILE X 236 " pdb=" CB ILE X 236 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA PRO X 237 " pdb=" N PRO X 237 " pdb=" C PRO X 237 " pdb=" CB PRO X 237 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 1458 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 53 " -0.016 2.00e-02 2.50e+03 1.32e-02 3.06e+00 pdb=" CG PHE H 53 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 53 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 53 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE H 53 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 53 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 53 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 91 " -0.128 9.50e-02 1.11e+02 5.73e-02 2.03e+00 pdb=" NE ARG C 91 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG C 91 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 91 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 91 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 52 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO H 52A" -0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 52A" 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 52A" 0.019 5.00e-02 4.00e+02 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 507 2.73 - 3.27: 8892 3.27 - 3.81: 15717 3.81 - 4.36: 19454 4.36 - 4.90: 33932 Nonbonded interactions: 78502 Sorted by model distance: nonbonded pdb=" O TRP B 100F" pdb=" OH TYR C 36 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR D 35 " pdb=" O3 FUC A 2 " model vdw 2.278 3.040 nonbonded pdb=" OE2 GLU B 6 " pdb=" N GLY B 106 " model vdw 2.354 3.120 nonbonded pdb=" OD1 ASP D 72 " pdb=" OG SER D 74 " model vdw 2.357 3.040 nonbonded pdb=" OD1 ASP X 224 " pdb=" NZ LYS X 286 " model vdw 2.359 3.120 ... (remaining 78497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.200 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.004 0.036 9747 Z= 0.174 Angle : 0.626 11.402 13239 Z= 0.334 Chirality : 0.044 0.156 1461 Planarity : 0.004 0.057 1675 Dihedral : 10.978 79.912 3561 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.19 % Allowed : 3.77 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.43 (0.25), residues: 1208 helix: -3.53 (0.96), residues: 13 sheet: 0.36 (0.22), residues: 526 loop : 0.46 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 66B TYR 0.016 0.002 TYR I 91 PHE 0.030 0.002 PHE H 53 TRP 0.012 0.002 TRP B 47 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9732) covalent geometry : angle 0.62431 (13207) SS BOND : bond 0.00436 ( 13) SS BOND : angle 0.83022 ( 26) hydrogen bonds : bond 0.16544 ( 344) hydrogen bonds : angle 8.28576 ( 831) link_BETA1-6 : bond 0.00408 ( 1) link_BETA1-6 : angle 2.19455 ( 3) link_NAG-ASN : bond 0.00504 ( 1) link_NAG-ASN : angle 1.73006 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.250 Fit side-chains REVERT: B 3 GLN cc_start: 0.7892 (tt0) cc_final: 0.7601 (pt0) REVERT: B 100 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7971 (mt-10) REVERT: C 31 SER cc_start: 0.8995 (m) cc_final: 0.8659 (p) REVERT: C 72 THR cc_start: 0.8572 (m) cc_final: 0.8156 (p) REVERT: D 34 TYR cc_start: 0.8986 (m-80) cc_final: 0.8780 (m-80) REVERT: D 57 THR cc_start: 0.8472 (p) cc_final: 0.8189 (p) REVERT: D 58 TYR cc_start: 0.7885 (m-80) cc_final: 0.7384 (m-80) REVERT: D 63 LEU cc_start: 0.6019 (mt) cc_final: 0.5817 (mp) REVERT: D 110 THR cc_start: 0.9030 (m) cc_final: 0.8828 (p) REVERT: F 30 ASN cc_start: 0.8327 (m-40) cc_final: 0.8108 (m-40) REVERT: H 75 THR cc_start: 0.8589 (p) cc_final: 0.8375 (t) REVERT: I 103 LYS cc_start: 0.8374 (tttt) cc_final: 0.8123 (ttmm) REVERT: X 37 ASN cc_start: 0.7610 (t0) cc_final: 0.7322 (p0) REVERT: X 45 THR cc_start: 0.8299 (m) cc_final: 0.8018 (p) REVERT: X 108 LYS cc_start: 0.8750 (mttt) cc_final: 0.8464 (mttp) REVERT: X 120 LYS cc_start: 0.7804 (mttt) cc_final: 0.7567 (mtmm) REVERT: X 255 ASN cc_start: 0.7170 (m-40) cc_final: 0.6881 (m110) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.0974 time to fit residues: 36.5996 Evaluate side-chains 185 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN E 6 GLN F 52AASN G 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122670 restraints weight = 12683.976| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.43 r_work: 0.3349 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9747 Z= 0.147 Angle : 0.587 6.837 13239 Z= 0.311 Chirality : 0.046 0.161 1461 Planarity : 0.004 0.043 1675 Dihedral : 5.232 56.882 1369 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.36 % Allowed : 11.03 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.55 (0.25), residues: 1208 helix: -3.36 (0.97), residues: 12 sheet: 0.63 (0.23), residues: 510 loop : 0.35 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 61 TYR 0.025 0.002 TYR C 49 PHE 0.019 0.002 PHE C 83 TRP 0.019 0.002 TRP E 35 HIS 0.002 0.001 HIS X 217 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9732) covalent geometry : angle 0.58560 (13207) SS BOND : bond 0.00399 ( 13) SS BOND : angle 0.81011 ( 26) hydrogen bonds : bond 0.03423 ( 344) hydrogen bonds : angle 6.39239 ( 831) link_BETA1-6 : bond 0.00727 ( 1) link_BETA1-6 : angle 1.66404 ( 3) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 1.66664 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.350 Fit side-chains REVERT: B 30 SER cc_start: 0.8951 (p) cc_final: 0.8741 (m) REVERT: B 100 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 31 SER cc_start: 0.8980 (m) cc_final: 0.8687 (p) REVERT: C 72 THR cc_start: 0.8515 (m) cc_final: 0.8093 (p) REVERT: C 78 LEU cc_start: 0.7372 (tp) cc_final: 0.6804 (mt) REVERT: D 30 SER cc_start: 0.8354 (p) cc_final: 0.8079 (m) REVERT: D 34 TYR cc_start: 0.9096 (m-80) cc_final: 0.8791 (m-80) REVERT: E 14 SER cc_start: 0.7573 (m) cc_final: 0.7373 (t) REVERT: E 36 TYR cc_start: 0.8693 (m-80) cc_final: 0.8417 (m-80) REVERT: E 61 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7302 (mtm110) REVERT: F 30 ASN cc_start: 0.8234 (m-40) cc_final: 0.8026 (m-40) REVERT: G 52 ASP cc_start: 0.8792 (p0) cc_final: 0.8557 (p0) REVERT: H 75 THR cc_start: 0.8677 (p) cc_final: 0.8399 (t) REVERT: I 42 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8043 (mptt) REVERT: X 37 ASN cc_start: 0.7778 (t0) cc_final: 0.7497 (p0) REVERT: X 108 LYS cc_start: 0.8867 (mttt) cc_final: 0.8654 (mtpp) REVERT: X 120 LYS cc_start: 0.8096 (mttt) cc_final: 0.7784 (mtmm) outliers start: 25 outliers final: 18 residues processed: 223 average time/residue: 0.0933 time to fit residues: 29.1790 Evaluate side-chains 200 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 292 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 60 optimal weight: 0.0670 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 98 optimal weight: 0.1980 chunk 94 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN F 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120749 restraints weight = 12630.618| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.31 r_work: 0.3328 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9747 Z= 0.151 Angle : 0.561 9.988 13239 Z= 0.295 Chirality : 0.045 0.196 1461 Planarity : 0.004 0.037 1675 Dihedral : 5.033 56.212 1369 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.54 % Allowed : 13.20 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.49 (0.25), residues: 1208 helix: -3.32 (0.95), residues: 12 sheet: 0.62 (0.23), residues: 502 loop : 0.29 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 94 TYR 0.016 0.002 TYR X 90 PHE 0.014 0.002 PHE X 151 TRP 0.020 0.002 TRP E 35 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9732) covalent geometry : angle 0.55974 (13207) SS BOND : bond 0.00361 ( 13) SS BOND : angle 0.75145 ( 26) hydrogen bonds : bond 0.03273 ( 344) hydrogen bonds : angle 6.05544 ( 831) link_BETA1-6 : bond 0.00504 ( 1) link_BETA1-6 : angle 1.48470 ( 3) link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 1.33464 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.354 Fit side-chains REVERT: B 7 ASN cc_start: 0.7606 (p0) cc_final: 0.7273 (p0) REVERT: B 34 MET cc_start: 0.7742 (mmm) cc_final: 0.7491 (mmt) REVERT: B 100 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7797 (mt-10) REVERT: C 31 SER cc_start: 0.9037 (m) cc_final: 0.8747 (p) REVERT: C 52 SER cc_start: 0.8510 (t) cc_final: 0.7917 (p) REVERT: C 72 THR cc_start: 0.8622 (m) cc_final: 0.8241 (p) REVERT: C 78 LEU cc_start: 0.7308 (tp) cc_final: 0.6777 (mt) REVERT: D 30 SER cc_start: 0.8389 (p) cc_final: 0.8134 (m) REVERT: D 34 TYR cc_start: 0.9081 (m-80) cc_final: 0.8794 (m-80) REVERT: E 36 TYR cc_start: 0.8726 (m-80) cc_final: 0.8302 (m-80) REVERT: E 61 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7557 (mtm110) REVERT: H 75 THR cc_start: 0.8719 (p) cc_final: 0.8414 (t) REVERT: I 42 LYS cc_start: 0.8589 (mmtt) cc_final: 0.7986 (mptt) REVERT: I 61 ARG cc_start: 0.7978 (ptt90) cc_final: 0.7751 (ptt180) REVERT: X 37 ASN cc_start: 0.7843 (t0) cc_final: 0.7359 (p0) REVERT: X 120 LYS cc_start: 0.8166 (mttt) cc_final: 0.7744 (mtmm) outliers start: 27 outliers final: 20 residues processed: 213 average time/residue: 0.0911 time to fit residues: 27.4165 Evaluate side-chains 199 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113333 restraints weight = 12886.988| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.65 r_work: 0.3211 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9747 Z= 0.210 Angle : 0.592 7.053 13239 Z= 0.312 Chirality : 0.046 0.152 1461 Planarity : 0.004 0.040 1675 Dihedral : 5.140 55.783 1369 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.15 % Allowed : 13.10 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.42 (0.25), residues: 1208 helix: -3.51 (0.85), residues: 12 sheet: 0.54 (0.23), residues: 520 loop : 0.26 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 18 TYR 0.018 0.002 TYR X 90 PHE 0.017 0.002 PHE X 132 TRP 0.022 0.002 TRP E 35 HIS 0.003 0.001 HIS X 217 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 9732) covalent geometry : angle 0.59102 (13207) SS BOND : bond 0.00502 ( 13) SS BOND : angle 0.90764 ( 26) hydrogen bonds : bond 0.03325 ( 344) hydrogen bonds : angle 6.07340 ( 831) link_BETA1-6 : bond 0.00505 ( 1) link_BETA1-6 : angle 1.48735 ( 3) link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 1.26962 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.387 Fit side-chains REVERT: B 34 MET cc_start: 0.7983 (mmm) cc_final: 0.7609 (mmt) REVERT: B 100 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 105 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7666 (mm-40) REVERT: C 31 SER cc_start: 0.9164 (m) cc_final: 0.8799 (p) REVERT: C 52 SER cc_start: 0.8563 (t) cc_final: 0.8021 (p) REVERT: C 72 THR cc_start: 0.8816 (m) cc_final: 0.8481 (p) REVERT: C 78 LEU cc_start: 0.7203 (tp) cc_final: 0.6517 (mt) REVERT: D 30 SER cc_start: 0.8635 (p) cc_final: 0.8432 (t) REVERT: D 34 TYR cc_start: 0.9057 (m-80) cc_final: 0.8729 (m-80) REVERT: E 36 TYR cc_start: 0.8817 (m-80) cc_final: 0.8270 (m-80) REVERT: F 3 GLN cc_start: 0.8394 (pt0) cc_final: 0.8053 (pt0) REVERT: F 30 ASN cc_start: 0.8180 (m-40) cc_final: 0.7980 (m-40) REVERT: H 75 THR cc_start: 0.8655 (p) cc_final: 0.8341 (t) REVERT: I 42 LYS cc_start: 0.8421 (mmtt) cc_final: 0.7691 (mptt) REVERT: I 61 ARG cc_start: 0.7782 (ptt90) cc_final: 0.7076 (ptt180) REVERT: X 37 ASN cc_start: 0.7965 (t0) cc_final: 0.7566 (p0) REVERT: X 120 LYS cc_start: 0.8009 (mttt) cc_final: 0.7392 (mtmm) REVERT: X 131 ASN cc_start: 0.8272 (m110) cc_final: 0.8004 (m110) REVERT: X 164 ASN cc_start: 0.6746 (t0) cc_final: 0.6525 (t0) outliers start: 44 outliers final: 32 residues processed: 209 average time/residue: 0.0977 time to fit residues: 28.4758 Evaluate side-chains 210 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 263 ILE Chi-restraints excluded: chain X residue 293 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113046 restraints weight = 12803.254| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.76 r_work: 0.3232 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9747 Z= 0.141 Angle : 0.547 7.219 13239 Z= 0.287 Chirality : 0.045 0.156 1461 Planarity : 0.004 0.039 1675 Dihedral : 5.031 56.816 1369 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.20 % Allowed : 14.14 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.43 (0.25), residues: 1208 helix: -3.30 (0.94), residues: 12 sheet: 0.54 (0.23), residues: 516 loop : 0.28 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 61 TYR 0.017 0.001 TYR X 90 PHE 0.015 0.002 PHE X 151 TRP 0.015 0.001 TRP E 35 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9732) covalent geometry : angle 0.54618 (13207) SS BOND : bond 0.00328 ( 13) SS BOND : angle 0.75715 ( 26) hydrogen bonds : bond 0.02975 ( 344) hydrogen bonds : angle 5.85937 ( 831) link_BETA1-6 : bond 0.00610 ( 1) link_BETA1-6 : angle 1.46737 ( 3) link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 1.12653 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.374 Fit side-chains REVERT: B 34 MET cc_start: 0.7778 (mmm) cc_final: 0.7463 (mmp) REVERT: B 100 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7767 (mt-10) REVERT: B 105 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7545 (mm-40) REVERT: C 31 SER cc_start: 0.9102 (m) cc_final: 0.8734 (p) REVERT: C 52 SER cc_start: 0.8541 (t) cc_final: 0.7996 (p) REVERT: C 72 THR cc_start: 0.8760 (m) cc_final: 0.8408 (p) REVERT: C 78 LEU cc_start: 0.7210 (tp) cc_final: 0.6572 (mt) REVERT: E 36 TYR cc_start: 0.8632 (m-80) cc_final: 0.7951 (m-80) REVERT: F 3 GLN cc_start: 0.8423 (pt0) cc_final: 0.8040 (pt0) REVERT: F 25 SER cc_start: 0.7416 (t) cc_final: 0.6982 (m) REVERT: H 75 THR cc_start: 0.8691 (p) cc_final: 0.8371 (t) REVERT: I 42 LYS cc_start: 0.8365 (mmtt) cc_final: 0.7627 (mptt) REVERT: X 37 ASN cc_start: 0.7903 (t0) cc_final: 0.7595 (p0) REVERT: X 120 LYS cc_start: 0.7949 (mttt) cc_final: 0.7346 (mtmm) REVERT: X 164 ASN cc_start: 0.6742 (t0) cc_final: 0.6501 (t0) outliers start: 34 outliers final: 25 residues processed: 204 average time/residue: 0.0963 time to fit residues: 27.6878 Evaluate side-chains 200 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 100 GLN Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 69 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN X 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112555 restraints weight = 12730.764| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.74 r_work: 0.3225 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9747 Z= 0.152 Angle : 0.548 6.859 13239 Z= 0.287 Chirality : 0.045 0.153 1461 Planarity : 0.004 0.036 1675 Dihedral : 4.980 56.713 1369 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.39 % Allowed : 15.46 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.45 (0.25), residues: 1208 helix: -2.70 (1.25), residues: 12 sheet: 0.56 (0.23), residues: 516 loop : 0.27 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 61 TYR 0.018 0.002 TYR X 90 PHE 0.016 0.002 PHE D 48 TRP 0.012 0.001 TRP B 47 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9732) covalent geometry : angle 0.54727 (13207) SS BOND : bond 0.00365 ( 13) SS BOND : angle 0.74751 ( 26) hydrogen bonds : bond 0.02937 ( 344) hydrogen bonds : angle 5.79235 ( 831) link_BETA1-6 : bond 0.00611 ( 1) link_BETA1-6 : angle 1.44515 ( 3) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 1.10134 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.353 Fit side-chains REVERT: B 34 MET cc_start: 0.7849 (mmm) cc_final: 0.7399 (mmt) REVERT: B 105 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7567 (mm-40) REVERT: C 31 SER cc_start: 0.9107 (m) cc_final: 0.8747 (p) REVERT: C 52 SER cc_start: 0.8581 (t) cc_final: 0.8044 (p) REVERT: C 78 LEU cc_start: 0.7114 (tp) cc_final: 0.6480 (mt) REVERT: E 36 TYR cc_start: 0.8646 (m-80) cc_final: 0.7959 (m-80) REVERT: F 3 GLN cc_start: 0.8319 (pt0) cc_final: 0.7954 (pt0) REVERT: F 25 SER cc_start: 0.7449 (t) cc_final: 0.7020 (m) REVERT: F 43 LYS cc_start: 0.7076 (mmtm) cc_final: 0.6690 (mmtm) REVERT: F 66 ARG cc_start: 0.8140 (mtm110) cc_final: 0.7887 (mtm110) REVERT: H 75 THR cc_start: 0.8731 (p) cc_final: 0.8400 (t) REVERT: I 42 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7613 (mptt) REVERT: X 37 ASN cc_start: 0.7935 (t0) cc_final: 0.7657 (p0) REVERT: X 120 LYS cc_start: 0.7982 (mttt) cc_final: 0.7372 (mtmm) REVERT: X 164 ASN cc_start: 0.6804 (t0) cc_final: 0.6567 (t0) outliers start: 36 outliers final: 30 residues processed: 201 average time/residue: 0.0965 time to fit residues: 27.0616 Evaluate side-chains 207 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.0050 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113154 restraints weight = 12698.210| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.80 r_work: 0.3245 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9747 Z= 0.118 Angle : 0.533 6.526 13239 Z= 0.278 Chirality : 0.044 0.155 1461 Planarity : 0.004 0.039 1675 Dihedral : 4.889 57.436 1369 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.02 % Allowed : 15.74 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.53 (0.26), residues: 1208 helix: -2.30 (1.51), residues: 12 sheet: 0.63 (0.24), residues: 515 loop : 0.30 (0.26), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 61 TYR 0.017 0.001 TYR X 90 PHE 0.015 0.001 PHE D 78 TRP 0.009 0.001 TRP B 47 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9732) covalent geometry : angle 0.53185 (13207) SS BOND : bond 0.00281 ( 13) SS BOND : angle 0.63366 ( 26) hydrogen bonds : bond 0.02734 ( 344) hydrogen bonds : angle 5.62929 ( 831) link_BETA1-6 : bond 0.00609 ( 1) link_BETA1-6 : angle 1.40159 ( 3) link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 1.04820 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.308 Fit side-chains REVERT: B 34 MET cc_start: 0.7859 (mmm) cc_final: 0.7422 (mmt) REVERT: B 105 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7516 (mm-40) REVERT: C 31 SER cc_start: 0.9079 (m) cc_final: 0.8711 (p) REVERT: C 52 SER cc_start: 0.8542 (t) cc_final: 0.7997 (p) REVERT: C 78 LEU cc_start: 0.7155 (tp) cc_final: 0.6558 (mt) REVERT: E 36 TYR cc_start: 0.8562 (m-80) cc_final: 0.7896 (m-80) REVERT: F 3 GLN cc_start: 0.8286 (pt0) cc_final: 0.7923 (pt0) REVERT: F 25 SER cc_start: 0.7377 (t) cc_final: 0.6964 (m) REVERT: F 66 ARG cc_start: 0.8094 (mtm110) cc_final: 0.7856 (mtm110) REVERT: G 17 LYS cc_start: 0.7406 (ttmm) cc_final: 0.7154 (ptpt) REVERT: H 75 THR cc_start: 0.8712 (p) cc_final: 0.8385 (t) REVERT: I 42 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7733 (mptt) REVERT: I 61 ARG cc_start: 0.7634 (ptt90) cc_final: 0.7288 (ptt180) REVERT: X 36 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7645 (t) REVERT: X 37 ASN cc_start: 0.7998 (t0) cc_final: 0.7693 (p0) REVERT: X 120 LYS cc_start: 0.7921 (mttt) cc_final: 0.7278 (mtmm) REVERT: X 164 ASN cc_start: 0.6733 (t0) cc_final: 0.6465 (t0) outliers start: 32 outliers final: 24 residues processed: 193 average time/residue: 0.0991 time to fit residues: 26.6467 Evaluate side-chains 196 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 285 ILE Chi-restraints excluded: chain X residue 294 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 43 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.140140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.113221 restraints weight = 12764.887| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.81 r_work: 0.3248 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9747 Z= 0.120 Angle : 0.534 6.466 13239 Z= 0.278 Chirality : 0.044 0.153 1461 Planarity : 0.004 0.038 1675 Dihedral : 4.869 57.334 1369 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.11 % Allowed : 15.83 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.54 (0.26), residues: 1208 helix: -2.21 (1.53), residues: 12 sheet: 0.65 (0.24), residues: 513 loop : 0.29 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 61 TYR 0.016 0.001 TYR X 90 PHE 0.016 0.001 PHE D 78 TRP 0.033 0.001 TRP E 35 HIS 0.002 0.000 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9732) covalent geometry : angle 0.53361 (13207) SS BOND : bond 0.00292 ( 13) SS BOND : angle 0.65397 ( 26) hydrogen bonds : bond 0.02741 ( 344) hydrogen bonds : angle 5.59596 ( 831) link_BETA1-6 : bond 0.00649 ( 1) link_BETA1-6 : angle 1.36466 ( 3) link_NAG-ASN : bond 0.00038 ( 1) link_NAG-ASN : angle 0.97361 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.352 Fit side-chains REVERT: B 34 MET cc_start: 0.7940 (mmm) cc_final: 0.7519 (mmt) REVERT: B 105 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7528 (mm-40) REVERT: C 31 SER cc_start: 0.9072 (m) cc_final: 0.8695 (p) REVERT: C 78 LEU cc_start: 0.7129 (tp) cc_final: 0.6542 (mt) REVERT: D 46 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7958 (mt-10) REVERT: E 36 TYR cc_start: 0.8592 (m-80) cc_final: 0.7812 (m-80) REVERT: F 25 SER cc_start: 0.7395 (t) cc_final: 0.6989 (m) REVERT: F 66 ARG cc_start: 0.8145 (mtm110) cc_final: 0.7912 (mtm110) REVERT: H 75 THR cc_start: 0.8721 (p) cc_final: 0.8384 (t) REVERT: I 42 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7706 (mptt) REVERT: I 61 ARG cc_start: 0.7644 (ptt90) cc_final: 0.7304 (ptt180) REVERT: X 36 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7673 (t) REVERT: X 37 ASN cc_start: 0.7993 (t0) cc_final: 0.7706 (p0) REVERT: X 120 LYS cc_start: 0.7959 (mttt) cc_final: 0.7328 (mtmm) REVERT: X 164 ASN cc_start: 0.6761 (t0) cc_final: 0.6487 (t0) outliers start: 33 outliers final: 29 residues processed: 194 average time/residue: 0.0916 time to fit residues: 25.3519 Evaluate side-chains 201 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 285 ILE Chi-restraints excluded: chain X residue 294 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112583 restraints weight = 12721.951| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.80 r_work: 0.3237 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9747 Z= 0.136 Angle : 0.544 6.936 13239 Z= 0.283 Chirality : 0.044 0.152 1461 Planarity : 0.004 0.041 1675 Dihedral : 4.882 57.912 1369 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.30 % Allowed : 16.12 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.53 (0.26), residues: 1208 helix: -2.34 (1.47), residues: 12 sheet: 0.66 (0.24), residues: 513 loop : 0.28 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 61 TYR 0.016 0.001 TYR X 90 PHE 0.017 0.001 PHE D 78 TRP 0.050 0.002 TRP E 35 HIS 0.002 0.000 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9732) covalent geometry : angle 0.54268 (13207) SS BOND : bond 0.00341 ( 13) SS BOND : angle 0.72408 ( 26) hydrogen bonds : bond 0.02802 ( 344) hydrogen bonds : angle 5.59888 ( 831) link_BETA1-6 : bond 0.00507 ( 1) link_BETA1-6 : angle 1.31781 ( 3) link_NAG-ASN : bond 0.00072 ( 1) link_NAG-ASN : angle 1.05618 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.306 Fit side-chains REVERT: B 34 MET cc_start: 0.7977 (mmm) cc_final: 0.7541 (mmt) REVERT: B 105 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7556 (mm-40) REVERT: C 31 SER cc_start: 0.9080 (m) cc_final: 0.8707 (p) REVERT: C 78 LEU cc_start: 0.7085 (tp) cc_final: 0.6515 (mt) REVERT: D 46 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7938 (mt-10) REVERT: E 36 TYR cc_start: 0.8618 (m-80) cc_final: 0.7858 (m-80) REVERT: F 25 SER cc_start: 0.7414 (t) cc_final: 0.6990 (m) REVERT: F 66 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7984 (mtm110) REVERT: H 75 THR cc_start: 0.8721 (p) cc_final: 0.8386 (t) REVERT: I 42 LYS cc_start: 0.8330 (mmtt) cc_final: 0.7716 (mptt) REVERT: I 61 ARG cc_start: 0.7627 (ptt90) cc_final: 0.7284 (ptt180) REVERT: X 36 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7651 (t) REVERT: X 37 ASN cc_start: 0.7995 (t0) cc_final: 0.7725 (p0) REVERT: X 120 LYS cc_start: 0.7943 (mttt) cc_final: 0.7303 (mtmm) REVERT: X 164 ASN cc_start: 0.6752 (t0) cc_final: 0.6488 (t0) outliers start: 35 outliers final: 32 residues processed: 193 average time/residue: 0.0840 time to fit residues: 23.3182 Evaluate side-chains 204 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 285 ILE Chi-restraints excluded: chain X residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 114 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN D 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113459 restraints weight = 12699.209| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.80 r_work: 0.3251 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9747 Z= 0.121 Angle : 0.536 7.034 13239 Z= 0.279 Chirality : 0.044 0.154 1461 Planarity : 0.004 0.046 1675 Dihedral : 4.828 57.553 1369 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.30 % Allowed : 15.83 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.57 (0.25), residues: 1208 helix: -2.22 (1.52), residues: 12 sheet: 0.72 (0.24), residues: 513 loop : 0.28 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 61 TYR 0.019 0.001 TYR X 90 PHE 0.018 0.001 PHE D 78 TRP 0.030 0.001 TRP E 35 HIS 0.001 0.000 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9732) covalent geometry : angle 0.53542 (13207) SS BOND : bond 0.00297 ( 13) SS BOND : angle 0.72968 ( 26) hydrogen bonds : bond 0.02700 ( 344) hydrogen bonds : angle 5.54673 ( 831) link_BETA1-6 : bond 0.00600 ( 1) link_BETA1-6 : angle 1.35176 ( 3) link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 0.92931 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.342 Fit side-chains REVERT: B 34 MET cc_start: 0.7955 (mmm) cc_final: 0.7529 (mmt) REVERT: B 105 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7563 (mm-40) REVERT: C 31 SER cc_start: 0.9024 (m) cc_final: 0.8684 (p) REVERT: C 78 LEU cc_start: 0.7073 (tp) cc_final: 0.6541 (mt) REVERT: E 36 TYR cc_start: 0.8584 (m-80) cc_final: 0.7856 (m-80) REVERT: F 25 SER cc_start: 0.7420 (t) cc_final: 0.7003 (m) REVERT: F 66 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7970 (mtm110) REVERT: H 75 THR cc_start: 0.8729 (p) cc_final: 0.8398 (t) REVERT: I 18 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: I 42 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7732 (mptt) REVERT: I 61 ARG cc_start: 0.7619 (ptt90) cc_final: 0.7291 (ptt180) REVERT: X 36 THR cc_start: 0.8081 (OUTLIER) cc_final: 0.7741 (t) REVERT: X 37 ASN cc_start: 0.8005 (t0) cc_final: 0.7661 (p0) REVERT: X 120 LYS cc_start: 0.7939 (mttt) cc_final: 0.7299 (mtmm) REVERT: X 164 ASN cc_start: 0.6712 (t0) cc_final: 0.6459 (t0) outliers start: 35 outliers final: 31 residues processed: 188 average time/residue: 0.0904 time to fit residues: 24.1264 Evaluate side-chains 201 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain X residue 36 THR Chi-restraints excluded: chain X residue 122 SER Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 225 VAL Chi-restraints excluded: chain X residue 285 ILE Chi-restraints excluded: chain X residue 294 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112899 restraints weight = 12684.039| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.81 r_work: 0.3243 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9747 Z= 0.127 Angle : 0.537 7.407 13239 Z= 0.280 Chirality : 0.044 0.153 1461 Planarity : 0.004 0.045 1675 Dihedral : 4.819 57.939 1369 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.30 % Allowed : 15.65 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.13 % Cis-general : 0.09 % 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: 0.57 (0.26), residues: 1208 helix: -2.26 (1.52), residues: 12 sheet: 0.71 (0.24), residues: 513 loop : 0.28 (0.26), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 61 TYR 0.018 0.001 TYR X 90 PHE 0.017 0.001 PHE D 78 TRP 0.031 0.001 TRP E 35 HIS 0.001 0.000 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9732) covalent geometry : angle 0.53665 (13207) SS BOND : bond 0.00316 ( 13) SS BOND : angle 0.70874 ( 26) hydrogen bonds : bond 0.02742 ( 344) hydrogen bonds : angle 5.53116 ( 831) link_BETA1-6 : bond 0.00579 ( 1) link_BETA1-6 : angle 1.35689 ( 3) link_NAG-ASN : bond 0.00032 ( 1) link_NAG-ASN : angle 0.95946 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.31 seconds wall clock time: 38 minutes 10.62 seconds (2290.62 seconds total)