Starting phenix.real_space_refine on Fri Aug 22 15:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez7_28729/08_2025/8ez7_28729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez7_28729/08_2025/8ez7_28729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez7_28729/08_2025/8ez7_28729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez7_28729/08_2025/8ez7_28729.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez7_28729/08_2025/8ez7_28729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez7_28729/08_2025/8ez7_28729.cif" } resolution = 2.6 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= -0.001 sd= 0.202 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 28 5.16 5 C 3065 2.51 5 N 845 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4927 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 833 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 372} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.25, per 1000 atoms: 0.25 Number of scatterers: 4927 At special positions: 0 Unit cell: (95.4, 83.74, 89.04, 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 28 16.00 O 989 8.00 N 845 7.00 C 3065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " 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 ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 172.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 12 sheets defined 4.8% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.744A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.585A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.547A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.784A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.788A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 5.412A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.976A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.627A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N LEU L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N SER L 65 " --> pdb=" O LEU L 28 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.090A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.648A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 124 removed outlier: 5.343A pdb=" N THR A 138 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ARG A 118 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN A 136 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 134 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL A 122 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 132 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N CYS A 124 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 130 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.276A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.733A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.637A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.321A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.561A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 169 hydrogen bonds defined for protein. 429 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: 0.74 Time building geometry restraints manager: 0.46 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: 1609 1.34 - 1.46: 1256 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 5038 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.399 1.431 -0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C1 MAN B 5 " pdb=" C2 MAN B 5 " ideal model delta sigma weight residual 1.526 1.556 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.487 -0.018 1.28e-02 6.10e+03 2.03e+00 ... (remaining 5033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 6605 1.43 - 2.87: 191 2.87 - 4.30: 25 4.30 - 5.74: 7 5.74 - 7.17: 8 Bond angle restraints: 6836 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 115.33 4.51 1.25e+00 6.40e-01 1.30e+01 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 113.47 -2.77 1.22e+00 6.72e-01 5.14e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.51 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sigma weight residual 113.65 110.51 3.14 1.47e+00 4.63e-01 4.56e+00 ... (remaining 6831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 2853 23.46 - 46.93: 196 46.93 - 70.39: 28 70.39 - 93.85: 15 93.85 - 117.31: 11 Dihedral angle restraints: 3103 sinusoidal: 1336 harmonic: 1767 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 134.03 -41.03 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CA ALA A 177 " pdb=" C ALA A 177 " pdb=" N TRP A 178 " pdb=" CA TRP A 178 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C2 NAG A 503 " pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " pdb=" C5 NAG A 503 " ideal model delta sinusoidal sigma weight residual -62.96 54.35 -117.31 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 3100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 754 0.126 - 0.252: 5 0.252 - 0.378: 1 0.378 - 0.504: 0 0.504 - 0.630: 1 Chirality restraints: 761 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 758 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.121 2.00e-02 2.50e+03 1.70e-01 3.63e+02 pdb=" CG ASN A 329 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.299 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.06e+00 pdb=" N PRO A 126 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.61e+00 pdb=" N PRO L 95 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.017 5.00e-02 4.00e+02 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 325 2.73 - 3.27: 4643 3.27 - 3.81: 8984 3.81 - 4.36: 11401 4.36 - 4.90: 19097 Nonbonded interactions: 44450 Sorted by model distance: nonbonded pdb=" OG SER A 179 " pdb=" OE2 GLU A 227 " model vdw 2.185 3.040 nonbonded pdb=" OG SER L 27A" pdb=" O ASP A 309 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 309 " pdb=" OG SER A 311 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 399 " pdb=" OG SER A 457 " model vdw 2.259 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.290 3.040 ... (remaining 44445 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=0.34 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.320 Find NCS groups from input model: 0.030 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 0.085 5057 Z= 0.198 Angle : 0.733 23.370 6882 Z= 0.339 Chirality : 0.051 0.630 761 Planarity : 0.004 0.044 876 Dihedral : 18.250 117.313 1950 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.32 % Allowed : 16.76 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.10 (0.34), residues: 618 helix: 0.60 (2.68), residues: 6 sheet: -0.05 (0.32), residues: 249 loop : 0.04 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.013 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5038) covalent geometry : angle 0.61144 ( 6836) SS BOND : bond 0.00320 ( 11) SS BOND : angle 0.68859 ( 22) hydrogen bonds : bond 0.19115 ( 160) hydrogen bonds : angle 8.84799 ( 429) link_ALPHA1-2 : bond 0.00526 ( 1) link_ALPHA1-2 : angle 1.80415 ( 3) link_ALPHA1-3 : bond 0.00073 ( 1) link_ALPHA1-3 : angle 1.80432 ( 3) link_BETA1-4 : bond 0.00380 ( 2) link_BETA1-4 : angle 2.13839 ( 6) link_NAG-ASN : bond 0.02082 ( 4) link_NAG-ASN : angle 9.52468 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.184 Fit side-chains REVERT: A 277 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8125 (mt-10) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.4611 time to fit residues: 38.9653 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 370 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.111968 restraints weight = 4812.828| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.33 r_work: 0.3039 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5057 Z= 0.129 Angle : 0.608 10.869 6882 Z= 0.308 Chirality : 0.049 0.414 761 Planarity : 0.004 0.043 876 Dihedral : 13.122 103.532 873 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.64 % Allowed : 15.63 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.20 (0.33), residues: 618 helix: 0.26 (2.41), residues: 6 sheet: -0.04 (0.31), residues: 247 loop : -0.11 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.011 0.001 TYR A 121 PHE 0.012 0.001 PHE A 354 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5038) covalent geometry : angle 0.57740 ( 6836) SS BOND : bond 0.00221 ( 11) SS BOND : angle 0.59717 ( 22) hydrogen bonds : bond 0.03866 ( 160) hydrogen bonds : angle 6.78708 ( 429) link_ALPHA1-2 : bond 0.00701 ( 1) link_ALPHA1-2 : angle 1.58185 ( 3) link_ALPHA1-3 : bond 0.01004 ( 1) link_ALPHA1-3 : angle 1.88768 ( 3) link_BETA1-4 : bond 0.00450 ( 2) link_BETA1-4 : angle 2.01342 ( 6) link_NAG-ASN : bond 0.00934 ( 4) link_NAG-ASN : angle 4.22729 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.183 Fit side-chains REVERT: L 100 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: A 277 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 430 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7609 (mmt-90) outliers start: 14 outliers final: 8 residues processed: 83 average time/residue: 0.4393 time to fit residues: 38.0758 Evaluate side-chains 75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106414 restraints weight = 4780.873| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.48 r_work: 0.2990 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5057 Z= 0.164 Angle : 0.618 11.428 6882 Z= 0.316 Chirality : 0.049 0.408 761 Planarity : 0.004 0.043 876 Dihedral : 10.744 99.493 867 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.58 % Allowed : 16.01 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.20 (0.33), residues: 618 helix: 0.25 (2.37), residues: 6 sheet: -0.01 (0.31), residues: 232 loop : -0.14 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.014 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5038) covalent geometry : angle 0.58796 ( 6836) SS BOND : bond 0.00273 ( 11) SS BOND : angle 0.65417 ( 22) hydrogen bonds : bond 0.03853 ( 160) hydrogen bonds : angle 6.43599 ( 429) link_ALPHA1-2 : bond 0.00611 ( 1) link_ALPHA1-2 : angle 1.73659 ( 3) link_ALPHA1-3 : bond 0.00790 ( 1) link_ALPHA1-3 : angle 1.62112 ( 3) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 1.91512 ( 6) link_NAG-ASN : bond 0.00809 ( 4) link_NAG-ASN : angle 4.28557 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.184 Fit side-chains REVERT: A 277 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8077 (mt-10) REVERT: A 368 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7620 (mt-10) outliers start: 19 outliers final: 9 residues processed: 81 average time/residue: 0.4332 time to fit residues: 36.7224 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109761 restraints weight = 4818.149| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.39 r_work: 0.3027 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5057 Z= 0.153 Angle : 0.599 11.074 6882 Z= 0.306 Chirality : 0.048 0.411 761 Planarity : 0.004 0.043 876 Dihedral : 9.850 96.461 867 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.64 % Allowed : 16.95 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.27 (0.33), residues: 618 helix: 0.22 (2.37), residues: 6 sheet: -0.03 (0.31), residues: 232 loop : -0.20 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.012 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5038) covalent geometry : angle 0.56763 ( 6836) SS BOND : bond 0.00239 ( 11) SS BOND : angle 0.63441 ( 22) hydrogen bonds : bond 0.03399 ( 160) hydrogen bonds : angle 6.25306 ( 429) link_ALPHA1-2 : bond 0.00700 ( 1) link_ALPHA1-2 : angle 1.77458 ( 3) link_ALPHA1-3 : bond 0.01084 ( 1) link_ALPHA1-3 : angle 1.64163 ( 3) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 1.88301 ( 6) link_NAG-ASN : bond 0.00806 ( 4) link_NAG-ASN : angle 4.25940 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.152 Fit side-chains REVERT: L 100 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: A 277 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 368 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7504 (mt-10) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.5146 time to fit residues: 41.2706 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103228 restraints weight = 4881.618| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.50 r_work: 0.2929 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5057 Z= 0.246 Angle : 0.673 11.294 6882 Z= 0.346 Chirality : 0.051 0.420 761 Planarity : 0.005 0.045 876 Dihedral : 10.017 94.878 867 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.33 % Allowed : 16.20 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.43 (0.32), residues: 618 helix: 0.18 (2.40), residues: 6 sheet: -0.21 (0.31), residues: 224 loop : -0.27 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 38 TYR 0.015 0.002 TYR A 121 PHE 0.015 0.002 PHE A 354 TRP 0.013 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 5038) covalent geometry : angle 0.64103 ( 6836) SS BOND : bond 0.00384 ( 11) SS BOND : angle 0.82355 ( 22) hydrogen bonds : bond 0.03904 ( 160) hydrogen bonds : angle 6.41343 ( 429) link_ALPHA1-2 : bond 0.00453 ( 1) link_ALPHA1-2 : angle 2.08969 ( 3) link_ALPHA1-3 : bond 0.00617 ( 1) link_ALPHA1-3 : angle 1.78310 ( 3) link_BETA1-4 : bond 0.00238 ( 2) link_BETA1-4 : angle 2.09800 ( 6) link_NAG-ASN : bond 0.00853 ( 4) link_NAG-ASN : angle 4.47518 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.144 Fit side-chains REVERT: L 100 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: A 277 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8089 (mt-10) REVERT: A 368 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7652 (mt-10) outliers start: 23 outliers final: 13 residues processed: 85 average time/residue: 0.4323 time to fit residues: 38.5935 Evaluate side-chains 86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105374 restraints weight = 4874.872| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.49 r_work: 0.2968 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5057 Z= 0.175 Angle : 0.625 10.928 6882 Z= 0.321 Chirality : 0.049 0.409 761 Planarity : 0.004 0.045 876 Dihedral : 9.538 93.049 867 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.20 % Allowed : 17.70 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.36 (0.33), residues: 618 helix: 0.21 (2.40), residues: 6 sheet: -0.08 (0.32), residues: 232 loop : -0.27 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 430 TYR 0.012 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.016 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 5038) covalent geometry : angle 0.59406 ( 6836) SS BOND : bond 0.00250 ( 11) SS BOND : angle 0.92134 ( 22) hydrogen bonds : bond 0.03506 ( 160) hydrogen bonds : angle 6.25347 ( 429) link_ALPHA1-2 : bond 0.00592 ( 1) link_ALPHA1-2 : angle 1.92345 ( 3) link_ALPHA1-3 : bond 0.00962 ( 1) link_ALPHA1-3 : angle 1.57804 ( 3) link_BETA1-4 : bond 0.00383 ( 2) link_BETA1-4 : angle 1.90664 ( 6) link_NAG-ASN : bond 0.00791 ( 4) link_NAG-ASN : angle 4.27495 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.182 Fit side-chains REVERT: L 100 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: A 277 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8041 (mt-10) REVERT: A 368 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7661 (mt-10) outliers start: 17 outliers final: 11 residues processed: 78 average time/residue: 0.5013 time to fit residues: 40.7876 Evaluate side-chains 82 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104490 restraints weight = 4849.908| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.42 r_work: 0.2942 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5057 Z= 0.320 Angle : 0.734 11.286 6882 Z= 0.379 Chirality : 0.053 0.428 761 Planarity : 0.005 0.046 876 Dihedral : 10.105 92.779 867 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.95 % Allowed : 16.95 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.52 (0.32), residues: 618 helix: 0.15 (2.44), residues: 6 sheet: -0.20 (0.31), residues: 232 loop : -0.38 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 430 TYR 0.016 0.003 TYR A 121 PHE 0.015 0.003 PHE A 354 TRP 0.015 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00723 ( 5038) covalent geometry : angle 0.70053 ( 6836) SS BOND : bond 0.00531 ( 11) SS BOND : angle 1.41351 ( 22) hydrogen bonds : bond 0.04202 ( 160) hydrogen bonds : angle 6.51664 ( 429) link_ALPHA1-2 : bond 0.00257 ( 1) link_ALPHA1-2 : angle 2.30136 ( 3) link_ALPHA1-3 : bond 0.00440 ( 1) link_ALPHA1-3 : angle 1.90103 ( 3) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 2.27181 ( 6) link_NAG-ASN : bond 0.00886 ( 4) link_NAG-ASN : angle 4.54528 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.186 Fit side-chains REVERT: L 100 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: A 162 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 368 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7629 (mt-10) outliers start: 21 outliers final: 12 residues processed: 85 average time/residue: 0.4162 time to fit residues: 36.9247 Evaluate side-chains 86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.110241 restraints weight = 4807.302| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.40 r_work: 0.3026 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5057 Z= 0.139 Angle : 0.604 10.561 6882 Z= 0.309 Chirality : 0.048 0.396 761 Planarity : 0.004 0.045 876 Dihedral : 9.089 89.024 867 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.64 % Allowed : 18.64 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.36 (0.33), residues: 618 helix: 0.17 (2.43), residues: 6 sheet: -0.10 (0.32), residues: 232 loop : -0.26 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.011 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.017 0.002 TRP A 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5038) covalent geometry : angle 0.57443 ( 6836) SS BOND : bond 0.00218 ( 11) SS BOND : angle 0.94552 ( 22) hydrogen bonds : bond 0.03230 ( 160) hydrogen bonds : angle 6.14314 ( 429) link_ALPHA1-2 : bond 0.00684 ( 1) link_ALPHA1-2 : angle 1.80703 ( 3) link_ALPHA1-3 : bond 0.01152 ( 1) link_ALPHA1-3 : angle 1.39577 ( 3) link_BETA1-4 : bond 0.00485 ( 2) link_BETA1-4 : angle 1.82099 ( 6) link_NAG-ASN : bond 0.00748 ( 4) link_NAG-ASN : angle 4.11448 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.107 Fit side-chains REVERT: L 100 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: A 277 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7845 (mt-10) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.4071 time to fit residues: 34.3988 Evaluate side-chains 79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.110945 restraints weight = 4776.758| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.36 r_work: 0.3016 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5057 Z= 0.148 Angle : 0.614 10.967 6882 Z= 0.314 Chirality : 0.048 0.385 761 Planarity : 0.004 0.045 876 Dihedral : 8.699 84.143 867 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.26 % Allowed : 19.02 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.32 (0.33), residues: 618 helix: 0.27 (2.44), residues: 6 sheet: -0.07 (0.32), residues: 232 loop : -0.23 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.011 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.014 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5038) covalent geometry : angle 0.58420 ( 6836) SS BOND : bond 0.00250 ( 11) SS BOND : angle 0.96077 ( 22) hydrogen bonds : bond 0.03279 ( 160) hydrogen bonds : angle 6.09045 ( 429) link_ALPHA1-2 : bond 0.00620 ( 1) link_ALPHA1-2 : angle 1.89936 ( 3) link_ALPHA1-3 : bond 0.00975 ( 1) link_ALPHA1-3 : angle 1.54581 ( 3) link_BETA1-4 : bond 0.00430 ( 2) link_BETA1-4 : angle 1.89157 ( 6) link_NAG-ASN : bond 0.00711 ( 4) link_NAG-ASN : angle 4.14035 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.108 Fit side-chains REVERT: L 100 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: A 277 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7937 (mt-10) outliers start: 12 outliers final: 9 residues processed: 78 average time/residue: 0.4504 time to fit residues: 36.5899 Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112243 restraints weight = 4783.958| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.40 r_work: 0.3031 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5057 Z= 0.125 Angle : 0.596 11.436 6882 Z= 0.301 Chirality : 0.046 0.336 761 Planarity : 0.004 0.045 876 Dihedral : 7.907 71.336 867 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.07 % Allowed : 19.96 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.28 (0.33), residues: 618 helix: 0.42 (2.42), residues: 6 sheet: -0.02 (0.32), residues: 237 loop : -0.23 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.010 0.001 TYR A 121 PHE 0.012 0.001 PHE A 354 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5038) covalent geometry : angle 0.56566 ( 6836) SS BOND : bond 0.00205 ( 11) SS BOND : angle 0.90966 ( 22) hydrogen bonds : bond 0.03090 ( 160) hydrogen bonds : angle 5.92427 ( 429) link_ALPHA1-2 : bond 0.00644 ( 1) link_ALPHA1-2 : angle 1.76134 ( 3) link_ALPHA1-3 : bond 0.01106 ( 1) link_ALPHA1-3 : angle 1.38872 ( 3) link_BETA1-4 : bond 0.00478 ( 2) link_BETA1-4 : angle 1.76208 ( 6) link_NAG-ASN : bond 0.00646 ( 4) link_NAG-ASN : angle 4.10788 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.115 Fit side-chains REVERT: L 100 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: A 277 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7851 (mt-10) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.4661 time to fit residues: 35.4586 Evaluate side-chains 70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 73 ASN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109585 restraints weight = 4859.730| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.40 r_work: 0.3021 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5057 Z= 0.168 Angle : 0.633 11.042 6882 Z= 0.322 Chirality : 0.047 0.231 761 Planarity : 0.004 0.045 876 Dihedral : 7.580 52.767 867 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.88 % Allowed : 20.15 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.27 (0.33), residues: 618 helix: 0.31 (2.43), residues: 6 sheet: -0.10 (0.32), residues: 226 loop : -0.16 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.013 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.016 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5038) covalent geometry : angle 0.59854 ( 6836) SS BOND : bond 0.00277 ( 11) SS BOND : angle 1.04481 ( 22) hydrogen bonds : bond 0.03373 ( 160) hydrogen bonds : angle 6.02965 ( 429) link_ALPHA1-2 : bond 0.00559 ( 1) link_ALPHA1-2 : angle 1.94788 ( 3) link_ALPHA1-3 : bond 0.00845 ( 1) link_ALPHA1-3 : angle 1.52346 ( 3) link_BETA1-4 : bond 0.00424 ( 2) link_BETA1-4 : angle 1.96110 ( 6) link_NAG-ASN : bond 0.00505 ( 4) link_NAG-ASN : angle 4.50876 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.63 seconds wall clock time: 32 minutes 31.74 seconds (1951.74 seconds total)