Starting phenix.real_space_refine on Wed Jun 3 11:40:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ao_67523/06_2026/21ao_67523.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ao_67523/06_2026/21ao_67523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21ao_67523/06_2026/21ao_67523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ao_67523/06_2026/21ao_67523.map" model { file = "/net/cci-nas-00/data/ceres_data/21ao_67523/06_2026/21ao_67523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ao_67523/06_2026/21ao_67523.cif" } resolution = 2.85 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= 0.043 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 32 5.16 5 C 2715 2.51 5 N 716 2.21 5 O 869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4332 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 982 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "B" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2415 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 295} Chain breaks: 1 Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.40, per 1000 atoms: 0.32 Number of scatterers: 4332 At special positions: 0 Unit cell: (55.1, 85.5, 109.25, 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 32 16.00 O 869 8.00 N 716 7.00 C 2715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 49 " distance=2.03 Simple disulfide: pdb=" SG CYS H 143 " - pdb=" SG CYS H 156 " distance=2.04 Simple disulfide: pdb=" SG CYS H 180 " - pdb=" SG CYS H 327 " distance=2.03 Simple disulfide: pdb=" SG CYS H 206 " - pdb=" SG CYS H 216 " distance=2.03 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 266 " distance=2.04 Simple disulfide: pdb=" SG CYS H 258 " - pdb=" SG CYS H 305 " distance=2.05 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 303 " distance=2.04 Simple disulfide: pdb=" SG CYS H 274 " - pdb=" SG CYS H 280 " distance=2.03 Simple disulfide: pdb=" SG CYS H 287 " - pdb=" SG CYS H 292 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 7 " " MAN C 4 " - " MAN C 5 " ALPHA1-6 " BMA C 3 " - " MAN C 4 " " MAN C 4 " - " MAN C 6 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN H 63 " " NAG D 1 " - " ASN H 33 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 194.7 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 13 sheets defined 16.8% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.582A pdb=" N ILE A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.842A pdb=" N LEU B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 53 removed outlier: 3.509A pdb=" N ARG H 53 " --> pdb=" O CYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 97 through 104 Processing helix chain 'H' and resid 160 through 163 removed outlier: 3.708A pdb=" N SER H 163 " --> pdb=" O SER H 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 163' Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 252 through 256 removed outlier: 3.833A pdb=" N PHE H 256 " --> pdb=" O SER H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 277 Processing helix chain 'H' and resid 285 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.527A pdb=" N SER A 71 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.789A pdb=" N TRP A 33 " --> pdb=" O HIS A 99 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 34 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.577A pdb=" N CYS A 96 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP A 115 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG A 98 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.855A pdb=" N SER B 7 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.828A pdb=" N GLN B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.828A pdb=" N GLN B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 70 through 71 removed outlier: 6.677A pdb=" N TYR H 70 " --> pdb=" O LEU H 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.632A pdb=" N SER H 81 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE H 129 " --> pdb=" O LEU H 173 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE H 175 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU H 131 " --> pdb=" O ILE H 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 147 through 149 Processing sheet with id=AB1, first strand: chain 'H' and resid 177 through 180 removed outlier: 6.699A pdb=" N MET H 334 " --> pdb=" O ILE H 208 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE H 208 " --> pdb=" O MET H 334 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR H 336 " --> pdb=" O CYS H 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 177 through 180 removed outlier: 3.674A pdb=" N CYS H 327 " --> pdb=" O ASP H 231 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA H 228 " --> pdb=" O MET H 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 244 through 248 Processing sheet with id=AB4, first strand: chain 'H' and resid 259 through 260 161 hydrogen bonds defined for protein. 396 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: 0.42 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1375 1.35 - 1.47: 1156 1.47 - 1.59: 1863 1.59 - 1.71: 0 1.71 - 1.84: 43 Bond restraints: 4437 Sorted by residual: bond pdb=" C5 MAN C 7 " pdb=" O5 MAN C 7 " ideal model delta sigma weight residual 1.418 1.448 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " ideal model delta sigma weight residual 1.526 1.553 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C5 MAN C 6 " pdb=" O5 MAN C 6 " ideal model delta sigma weight residual 1.418 1.443 -0.025 2.00e-02 2.50e+03 1.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 4432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 5816 1.48 - 2.96: 138 2.96 - 4.45: 37 4.45 - 5.93: 9 5.93 - 7.41: 6 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA CYS H 258 " pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " ideal model delta sigma weight residual 114.40 121.81 -7.41 2.30e+00 1.89e-01 1.04e+01 angle pdb=" N CYS H 258 " pdb=" CA CYS H 258 " pdb=" C CYS H 258 " ideal model delta sigma weight residual 108.79 113.64 -4.85 1.53e+00 4.27e-01 1.00e+01 angle pdb=" C ASP H 283 " pdb=" CA ASP H 283 " pdb=" CB ASP H 283 " ideal model delta sigma weight residual 110.42 115.58 -5.16 1.99e+00 2.53e-01 6.72e+00 angle pdb=" C MET H 284 " pdb=" N GLN H 285 " pdb=" CA GLN H 285 " ideal model delta sigma weight residual 121.54 126.45 -4.91 1.91e+00 2.74e-01 6.61e+00 angle pdb=" N GLY H 76 " pdb=" CA GLY H 76 " pdb=" C GLY H 76 " ideal model delta sigma weight residual 110.77 114.77 -4.00 1.59e+00 3.96e-01 6.33e+00 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 2600 21.69 - 43.38: 135 43.38 - 65.07: 21 65.07 - 86.76: 12 86.76 - 108.45: 4 Dihedral angle restraints: 2772 sinusoidal: 1224 harmonic: 1548 Sorted by residual: dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 303 " pdb=" CB CYS H 303 " ideal model delta sinusoidal sigma weight residual -86.00 -156.85 70.85 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA ARG H 304 " pdb=" C ARG H 304 " pdb=" N CYS H 305 " pdb=" CA CYS H 305 " ideal model delta harmonic sigma weight residual -180.00 -146.16 -33.84 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CB CYS H 258 " pdb=" SG CYS H 258 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual -86.00 -129.01 43.01 1 1.00e+01 1.00e-02 2.58e+01 ... (remaining 2769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 521 0.053 - 0.105: 107 0.105 - 0.158: 31 0.158 - 0.211: 2 0.211 - 0.263: 1 Chirality restraints: 662 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA CYS H 258 " pdb=" N CYS H 258 " pdb=" C CYS H 258 " pdb=" CB CYS H 258 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CB ILE H 25 " pdb=" CA ILE H 25 " pdb=" CG1 ILE H 25 " pdb=" CG2 ILE H 25 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 659 not shown) Planarity restraints: 765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 121 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO H 122 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 122 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 122 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 97 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO H 98 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO H 98 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 98 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 132 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO H 133 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 133 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 133 " -0.020 5.00e-02 4.00e+02 ... (remaining 762 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 728 2.77 - 3.31: 3587 3.31 - 3.84: 6883 3.84 - 4.37: 8338 4.37 - 4.90: 14740 Nonbonded interactions: 34276 Sorted by model distance: nonbonded pdb=" OG SER H 198 " pdb=" O ILE H 239 " model vdw 2.243 3.040 nonbonded pdb=" NH1 ARG A 59 " pdb=" OH TYR A 110 " model vdw 2.284 3.120 nonbonded pdb=" NH2 ARG H 77 " pdb=" O LEU H 95 " model vdw 2.376 3.120 nonbonded pdb=" OE2 GLU H 261 " pdb=" NH2 ARG H 281 " model vdw 2.433 3.120 nonbonded pdb=" O TYR A 109 " pdb=" OG SER B 91 " model vdw 2.448 3.040 ... (remaining 34271 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.010 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 0.032 4457 Z= 0.163 Angle : 0.657 7.410 6055 Z= 0.316 Chirality : 0.048 0.263 662 Planarity : 0.004 0.051 763 Dihedral : 14.225 108.445 1755 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.21 % Allowed : 0.00 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.22 (0.36), residues: 538 helix: 1.02 (0.67), residues: 68 sheet: 0.60 (0.43), residues: 165 loop : -0.84 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 324 TYR 0.011 0.001 TYR H 83 PHE 0.014 0.001 PHE H 130 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 4437) covalent geometry : angle 0.63775 / 0.31 ( 6006) SS BOND : bond 0.00772 / 0.38 ( 11) SS BOND : angle 1.99512 / 1.04 ( 22) hydrogen bonds : bond 0.22639 / 14.12 ( 148) hydrogen bonds : angle 8.31866 / 5.75 ( 396) link_ALPHA1-3 : bond 0.00195 / 0.10 ( 2) link_ALPHA1-3 : angle 2.14026 / 1.09 ( 6) link_ALPHA1-6 : bond 0.00275 / 0.14 ( 2) link_ALPHA1-6 : angle 1.83982 / 0.91 ( 6) link_BETA1-4 : bond 0.00208 / 0.10 ( 3) link_BETA1-4 : angle 1.71225 / 0.87 ( 9) link_NAG-ASN : bond 0.00040 / 0.02 ( 2) link_NAG-ASN : angle 1.35685 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.103 Fit side-chains REVERT: H 148 SER cc_start: 0.8942 (p) cc_final: 0.8697 (p) REVERT: H 151 GLU cc_start: 0.7842 (tp30) cc_final: 0.7637 (tp30) REVERT: H 207 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7839 (mtpm) REVERT: H 255 ASP cc_start: 0.7863 (m-30) cc_final: 0.7534 (m-30) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.5180 time to fit residues: 35.1998 Evaluate side-chains 59 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN H 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.106935 restraints weight = 4785.587| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.22 r_work: 0.3131 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4457 Z= 0.126 Angle : 0.561 5.261 6055 Z= 0.298 Chirality : 0.045 0.135 662 Planarity : 0.005 0.051 763 Dihedral : 9.292 77.297 766 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.06 % Allowed : 6.37 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.37), residues: 538 helix: 1.20 (0.69), residues: 70 sheet: 0.68 (0.43), residues: 167 loop : -0.63 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 77 TYR 0.012 0.001 TYR H 83 PHE 0.017 0.001 PHE H 130 TRP 0.010 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 4437) covalent geometry : angle 0.54038 / 0.29 ( 6006) SS BOND : bond 0.00794 / 0.40 ( 11) SS BOND : angle 1.75607 / 1.04 ( 22) hydrogen bonds : bond 0.04710 / 3.02 ( 148) hydrogen bonds : angle 5.86700 / 3.96 ( 396) link_ALPHA1-3 : bond 0.00627 / 0.33 ( 2) link_ALPHA1-3 : angle 1.75791 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00296 / 0.15 ( 2) link_ALPHA1-6 : angle 1.79470 / 0.88 ( 6) link_BETA1-4 : bond 0.00156 / 0.08 ( 3) link_BETA1-4 : angle 1.89399 / 0.93 ( 9) link_NAG-ASN : bond 0.00026 / 0.01 ( 2) link_NAG-ASN : angle 1.37482 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.151 Fit side-chains REVERT: A 11 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7974 (mmt) REVERT: B 103 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8822 (ttmm) REVERT: H 151 GLU cc_start: 0.8555 (tp30) cc_final: 0.8163 (tp30) REVERT: H 207 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7907 (mtpm) REVERT: H 255 ASP cc_start: 0.7909 (m-30) cc_final: 0.7177 (m-30) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.7704 time to fit residues: 45.1479 Evaluate side-chains 58 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.139712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.106250 restraints weight = 4714.775| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.20 r_work: 0.3123 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4457 Z= 0.141 Angle : 0.563 4.940 6055 Z= 0.297 Chirality : 0.046 0.198 662 Planarity : 0.005 0.050 763 Dihedral : 8.267 64.933 766 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.70 % Allowed : 8.07 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.37), residues: 538 helix: 1.32 (0.68), residues: 70 sheet: 0.74 (0.42), residues: 167 loop : -0.66 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 77 TYR 0.013 0.002 TYR H 83 PHE 0.019 0.001 PHE H 130 TRP 0.009 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 4437) covalent geometry : angle 0.53939 / 0.29 ( 6006) SS BOND : bond 0.00839 / 0.43 ( 11) SS BOND : angle 2.04460 / 1.28 ( 22) hydrogen bonds : bond 0.03789 / 2.49 ( 148) hydrogen bonds : angle 5.32956 / 3.58 ( 396) link_ALPHA1-3 : bond 0.00696 / 0.37 ( 2) link_ALPHA1-3 : angle 1.67401 / 0.88 ( 6) link_ALPHA1-6 : bond 0.00176 / 0.09 ( 2) link_ALPHA1-6 : angle 1.75120 / 0.84 ( 6) link_BETA1-4 : bond 0.00315 / 0.15 ( 3) link_BETA1-4 : angle 1.80487 / 0.88 ( 9) link_NAG-ASN : bond 0.00082 / 0.04 ( 2) link_NAG-ASN : angle 1.44004 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.180 Fit side-chains REVERT: A 67 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7703 (mm-40) REVERT: B 103 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8752 (ttmm) REVERT: H 91 ARG cc_start: 0.7418 (mtt90) cc_final: 0.6873 (mmp80) REVERT: H 151 GLU cc_start: 0.8570 (tp30) cc_final: 0.8186 (tp30) REVERT: H 207 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7941 (mtpm) REVERT: H 255 ASP cc_start: 0.7847 (m-30) cc_final: 0.7149 (m-30) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.6869 time to fit residues: 41.7417 Evaluate side-chains 63 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107640 restraints weight = 4704.914| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.22 r_work: 0.3144 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4457 Z= 0.110 Angle : 0.521 5.323 6055 Z= 0.273 Chirality : 0.045 0.161 662 Planarity : 0.005 0.050 763 Dihedral : 7.506 56.049 766 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.12 % Allowed : 9.34 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.37), residues: 538 helix: 1.49 (0.69), residues: 70 sheet: 0.77 (0.42), residues: 168 loop : -0.59 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 77 TYR 0.010 0.001 TYR H 83 PHE 0.017 0.001 PHE H 130 TRP 0.009 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 4437) covalent geometry : angle 0.49832 / 0.27 ( 6006) SS BOND : bond 0.00721 / 0.37 ( 11) SS BOND : angle 1.95388 / 1.26 ( 22) hydrogen bonds : bond 0.03195 / 2.09 ( 148) hydrogen bonds : angle 5.08228 / 3.38 ( 396) link_ALPHA1-3 : bond 0.00717 / 0.38 ( 2) link_ALPHA1-3 : angle 1.53505 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00236 / 0.11 ( 2) link_ALPHA1-6 : angle 1.69795 / 0.82 ( 6) link_BETA1-4 : bond 0.00276 / 0.13 ( 3) link_BETA1-4 : angle 1.75851 / 0.87 ( 9) link_NAG-ASN : bond 0.00038 / 0.02 ( 2) link_NAG-ASN : angle 1.39458 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.180 Fit side-chains REVERT: A 67 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7692 (mm-40) REVERT: B 103 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8732 (ttmm) REVERT: H 91 ARG cc_start: 0.7425 (mtt90) cc_final: 0.6869 (mmp80) REVERT: H 151 GLU cc_start: 0.8547 (tp30) cc_final: 0.8181 (tp30) REVERT: H 207 LYS cc_start: 0.8237 (mtpt) cc_final: 0.7868 (mtpm) REVERT: H 255 ASP cc_start: 0.7834 (m-30) cc_final: 0.7209 (m-30) outliers start: 10 outliers final: 4 residues processed: 57 average time/residue: 0.6851 time to fit residues: 40.2495 Evaluate side-chains 62 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 HIS H 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.108107 restraints weight = 4682.663| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.21 r_work: 0.3151 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4457 Z= 0.110 Angle : 0.522 5.662 6055 Z= 0.272 Chirality : 0.045 0.179 662 Planarity : 0.005 0.050 763 Dihedral : 6.936 49.910 766 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.55 % Allowed : 9.13 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.37), residues: 538 helix: 1.55 (0.69), residues: 70 sheet: 0.61 (0.42), residues: 175 loop : -0.53 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 77 TYR 0.011 0.001 TYR B 49 PHE 0.017 0.001 PHE H 130 TRP 0.009 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 4437) covalent geometry : angle 0.49897 / 0.27 ( 6006) SS BOND : bond 0.00704 / 0.36 ( 11) SS BOND : angle 1.98966 / 1.29 ( 22) hydrogen bonds : bond 0.03091 / 2.02 ( 148) hydrogen bonds : angle 5.00018 / 3.32 ( 396) link_ALPHA1-3 : bond 0.00765 / 0.40 ( 2) link_ALPHA1-3 : angle 1.51871 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00228 / 0.11 ( 2) link_ALPHA1-6 : angle 1.72047 / 0.83 ( 6) link_BETA1-4 : bond 0.00304 / 0.15 ( 3) link_BETA1-4 : angle 1.72139 / 0.86 ( 9) link_NAG-ASN : bond 0.00059 / 0.03 ( 2) link_NAG-ASN : angle 1.36180 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.174 Fit side-chains REVERT: A 67 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7716 (mm-40) REVERT: B 103 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8823 (ttmm) REVERT: H 91 ARG cc_start: 0.7421 (mtt90) cc_final: 0.6808 (mmp80) REVERT: H 151 GLU cc_start: 0.8558 (tp30) cc_final: 0.8195 (tp30) REVERT: H 207 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7834 (mtpm) REVERT: H 219 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: H 255 ASP cc_start: 0.7846 (m-30) cc_final: 0.7260 (m-30) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.6741 time to fit residues: 43.8262 Evaluate side-chains 66 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.140819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107082 restraints weight = 4812.756| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.26 r_work: 0.3136 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4457 Z= 0.123 Angle : 0.538 5.762 6055 Z= 0.281 Chirality : 0.045 0.177 662 Planarity : 0.005 0.050 763 Dihedral : 6.524 45.041 766 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.55 % Allowed : 9.77 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.37), residues: 538 helix: 1.52 (0.69), residues: 70 sheet: 0.61 (0.42), residues: 175 loop : -0.52 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 332 TYR 0.012 0.001 TYR H 83 PHE 0.017 0.001 PHE H 130 TRP 0.010 0.001 TRP H 141 HIS 0.005 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 4437) covalent geometry : angle 0.51496 / 0.27 ( 6006) SS BOND : bond 0.00739 / 0.38 ( 11) SS BOND : angle 2.06510 / 1.32 ( 22) hydrogen bonds : bond 0.03152 / 2.08 ( 148) hydrogen bonds : angle 5.00491 / 3.33 ( 396) link_ALPHA1-3 : bond 0.00796 / 0.42 ( 2) link_ALPHA1-3 : angle 1.54861 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00243 / 0.12 ( 2) link_ALPHA1-6 : angle 1.73902 / 0.85 ( 6) link_BETA1-4 : bond 0.00297 / 0.15 ( 3) link_BETA1-4 : angle 1.67983 / 0.84 ( 9) link_NAG-ASN : bond 0.00093 / 0.04 ( 2) link_NAG-ASN : angle 1.32495 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.111 Fit side-chains REVERT: A 67 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: B 103 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8822 (ttmm) REVERT: H 91 ARG cc_start: 0.7407 (mtt90) cc_final: 0.6789 (mmp80) REVERT: H 151 GLU cc_start: 0.8566 (tp30) cc_final: 0.8190 (tp30) REVERT: H 207 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7816 (mtpm) REVERT: H 219 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: H 255 ASP cc_start: 0.7788 (m-30) cc_final: 0.7153 (m-30) outliers start: 12 outliers final: 6 residues processed: 60 average time/residue: 0.5137 time to fit residues: 31.8185 Evaluate side-chains 65 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 240 MET Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 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 = 0.141672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108080 restraints weight = 4780.774| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.25 r_work: 0.3149 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4457 Z= 0.105 Angle : 0.519 5.383 6055 Z= 0.269 Chirality : 0.044 0.180 662 Planarity : 0.005 0.050 763 Dihedral : 6.038 40.230 766 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.34 % Allowed : 9.77 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.37), residues: 538 helix: 1.61 (0.69), residues: 70 sheet: 0.64 (0.42), residues: 175 loop : -0.47 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 171 TYR 0.011 0.001 TYR H 83 PHE 0.017 0.001 PHE H 130 TRP 0.009 0.001 TRP H 141 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 ( 4437) covalent geometry : angle 0.49744 / 0.26 ( 6006) SS BOND : bond 0.00691 / 0.36 ( 11) SS BOND : angle 1.91462 / 1.24 ( 22) hydrogen bonds : bond 0.02920 / 1.91 ( 148) hydrogen bonds : angle 4.90742 / 3.27 ( 396) link_ALPHA1-3 : bond 0.00888 / 0.47 ( 2) link_ALPHA1-3 : angle 1.46912 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00286 / 0.14 ( 2) link_ALPHA1-6 : angle 1.68854 / 0.83 ( 6) link_BETA1-4 : bond 0.00309 / 0.15 ( 3) link_BETA1-4 : angle 1.62910 / 0.81 ( 9) link_NAG-ASN : bond 0.00074 / 0.04 ( 2) link_NAG-ASN : angle 1.35344 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.106 Fit side-chains REVERT: A 67 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: B 103 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8720 (ttmm) REVERT: H 91 ARG cc_start: 0.7416 (mtt90) cc_final: 0.6774 (mmp80) REVERT: H 151 GLU cc_start: 0.8573 (tp30) cc_final: 0.8203 (tp30) REVERT: H 207 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7800 (mtpm) REVERT: H 255 ASP cc_start: 0.7752 (m-30) cc_final: 0.7155 (m-30) outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.6278 time to fit residues: 41.4153 Evaluate side-chains 65 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 240 MET Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.136688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103515 restraints weight = 4748.175| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.22 r_work: 0.3082 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 4457 Z= 0.253 Angle : 0.682 7.314 6055 Z= 0.354 Chirality : 0.050 0.182 662 Planarity : 0.005 0.050 763 Dihedral : 6.695 43.014 766 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.55 % Allowed : 9.77 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.36), residues: 538 helix: 1.08 (0.67), residues: 70 sheet: 0.62 (0.41), residues: 171 loop : -0.75 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.018 0.003 TYR H 83 PHE 0.019 0.002 PHE H 130 TRP 0.014 0.002 TRP H 141 HIS 0.008 0.002 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.25 ( 4437) covalent geometry : angle 0.65141 / 0.34 ( 6006) SS BOND : bond 0.00976 / 0.50 ( 11) SS BOND : angle 2.84144 / 1.77 ( 22) hydrogen bonds : bond 0.04213 / 2.81 ( 148) hydrogen bonds : angle 5.25796 / 3.54 ( 396) link_ALPHA1-3 : bond 0.00678 / 0.36 ( 2) link_ALPHA1-3 : angle 1.78359 / 0.96 ( 6) link_ALPHA1-6 : bond 0.00216 / 0.11 ( 2) link_ALPHA1-6 : angle 2.06690 / 0.99 ( 6) link_BETA1-4 : bond 0.00297 / 0.15 ( 3) link_BETA1-4 : angle 2.02098 / 1.03 ( 9) link_NAG-ASN : bond 0.00262 / 0.13 ( 2) link_NAG-ASN : angle 1.30019 / 0.67 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.152 Fit side-chains REVERT: A 67 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: H 151 GLU cc_start: 0.8564 (tp30) cc_final: 0.8180 (tp30) REVERT: H 207 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7890 (mtpm) REVERT: H 255 ASP cc_start: 0.7887 (m-30) cc_final: 0.7332 (m-30) outliers start: 12 outliers final: 6 residues processed: 59 average time/residue: 0.6908 time to fit residues: 42.0592 Evaluate side-chains 59 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.140320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106802 restraints weight = 4750.780| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.23 r_work: 0.3131 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4457 Z= 0.114 Angle : 0.545 6.047 6055 Z= 0.284 Chirality : 0.045 0.176 662 Planarity : 0.005 0.050 763 Dihedral : 6.045 38.271 766 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.91 % Allowed : 10.40 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.36), residues: 538 helix: 1.38 (0.68), residues: 70 sheet: 0.51 (0.41), residues: 175 loop : -0.61 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 132 TYR 0.011 0.001 TYR H 83 PHE 0.018 0.001 PHE H 130 TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 4437) covalent geometry : angle 0.52067 / 0.28 ( 6006) SS BOND : bond 0.00740 / 0.38 ( 11) SS BOND : angle 2.16291 / 1.39 ( 22) hydrogen bonds : bond 0.03076 / 2.02 ( 148) hydrogen bonds : angle 5.01976 / 3.36 ( 396) link_ALPHA1-3 : bond 0.00885 / 0.46 ( 2) link_ALPHA1-3 : angle 1.45061 / 0.77 ( 6) link_ALPHA1-6 : bond 0.00267 / 0.13 ( 2) link_ALPHA1-6 : angle 1.72765 / 0.85 ( 6) link_BETA1-4 : bond 0.00282 / 0.14 ( 3) link_BETA1-4 : angle 1.70582 / 0.85 ( 9) link_NAG-ASN : bond 0.00100 / 0.05 ( 2) link_NAG-ASN : angle 1.40631 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.191 Fit side-chains REVERT: A 67 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7765 (mm-40) REVERT: H 91 ARG cc_start: 0.7426 (mtt90) cc_final: 0.6914 (mmp80) REVERT: H 151 GLU cc_start: 0.8563 (tp30) cc_final: 0.8184 (tp30) REVERT: H 207 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7916 (mtpm) REVERT: H 255 ASP cc_start: 0.7885 (m-30) cc_final: 0.7326 (m-30) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.6079 time to fit residues: 36.4186 Evaluate side-chains 60 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 240 MET Chi-restraints excluded: chain H residue 248 VAL Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.0000 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 overall best weight: 0.2982 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.142575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.108984 restraints weight = 4754.107| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.26 r_work: 0.3168 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4457 Z= 0.090 Angle : 0.506 5.179 6055 Z= 0.262 Chirality : 0.044 0.166 662 Planarity : 0.005 0.050 763 Dihedral : 5.485 35.146 766 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.49 % Allowed : 10.83 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.37), residues: 538 helix: 1.67 (0.69), residues: 70 sheet: 0.57 (0.42), residues: 175 loop : -0.52 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 77 TYR 0.009 0.001 TYR H 83 PHE 0.017 0.001 PHE H 130 TRP 0.012 0.001 TRP A 47 HIS 0.003 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 4437) covalent geometry : angle 0.48603 / 0.26 ( 6006) SS BOND : bond 0.00662 / 0.34 ( 11) SS BOND : angle 1.78556 / 1.16 ( 22) hydrogen bonds : bond 0.02692 / 1.75 ( 148) hydrogen bonds : angle 4.83527 / 3.22 ( 396) link_ALPHA1-3 : bond 0.01009 / 0.53 ( 2) link_ALPHA1-3 : angle 1.40226 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00401 / 0.20 ( 2) link_ALPHA1-6 : angle 1.58938 / 0.79 ( 6) link_BETA1-4 : bond 0.00349 / 0.17 ( 3) link_BETA1-4 : angle 1.58063 / 0.79 ( 9) link_NAG-ASN : bond 0.00051 / 0.03 ( 2) link_NAG-ASN : angle 1.32368 / 0.67 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.187 Fit side-chains REVERT: H 91 ARG cc_start: 0.7500 (mtt90) cc_final: 0.6852 (mmp80) REVERT: H 151 GLU cc_start: 0.8518 (tp30) cc_final: 0.8136 (tp30) REVERT: H 207 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7839 (mtpm) REVERT: H 255 ASP cc_start: 0.7758 (m-30) cc_final: 0.7180 (m-30) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.5893 time to fit residues: 37.7430 Evaluate side-chains 63 residues out of total 471 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 258 CYS Chi-restraints excluded: chain H residue 305 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.0000 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.142728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109035 restraints weight = 4732.216| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.25 r_work: 0.3171 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4457 Z= 0.094 Angle : 0.515 5.956 6055 Z= 0.265 Chirality : 0.044 0.159 662 Planarity : 0.004 0.049 763 Dihedral : 5.290 32.606 766 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.06 % Allowed : 11.46 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.37), residues: 538 helix: 1.72 (0.69), residues: 70 sheet: 0.61 (0.42), residues: 175 loop : -0.48 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 59 TYR 0.010 0.001 TYR H 83 PHE 0.016 0.001 PHE H 130 TRP 0.011 0.001 TRP A 47 HIS 0.004 0.001 HIS H 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.09 ( 4437) covalent geometry : angle 0.49615 / 0.26 ( 6006) SS BOND : bond 0.00657 / 0.34 ( 11) SS BOND : angle 1.76694 / 1.13 ( 22) hydrogen bonds : bond 0.02683 / 1.75 ( 148) hydrogen bonds : angle 4.76871 / 3.17 ( 396) link_ALPHA1-3 : bond 0.01016 / 0.53 ( 2) link_ALPHA1-3 : angle 1.39755 / 0.74 ( 6) link_ALPHA1-6 : bond 0.00354 / 0.18 ( 2) link_ALPHA1-6 : angle 1.62979 / 0.80 ( 6) link_BETA1-4 : bond 0.00341 / 0.17 ( 3) link_BETA1-4 : angle 1.52423 / 0.77 ( 9) link_NAG-ASN : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : angle 1.23996 / 0.62 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.85 seconds wall clock time: 33 minutes 43.16 seconds (2023.16 seconds total)