Starting phenix.real_space_refine on Thu Jul 2 01:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_28729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_28729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_28729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_28729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_28729.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_28729.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ez7_28729/07_2026/8ez7_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 chiralities: 4 Time building chain proxies: 1.33, per 1000 atoms: 0.27 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: 0.43 Conformation dependent library (CDL) restraints added in 203.6 milliseconds 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: 0.16 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: 0.85 Time building geometry restraints manager: 0.55 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 - 16.53: 2550 16.53 - 33.06: 275 33.06 - 49.59: 79 49.59 - 66.12: 11 66.12 - 82.65: 7 Dihedral angle restraints: 2922 sinusoidal: 1155 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=" CA ASN H 100E" pdb=" C ASN H 100E" pdb=" N TRP H 100F" pdb=" CA TRP H 100F" ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 2919 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.040 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:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 15.088 82.645 1769 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 are 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/Z covalent geometry : bond 0.00414 / 0.20 ( 5038) covalent geometry : angle 0.61144 / 0.31 ( 6836) SS BOND : bond 0.00320 / 0.25 ( 11) SS BOND : angle 0.68859 / 0.46 ( 22) hydrogen bonds : bond 0.19115 / 12.88 ( 160) hydrogen bonds : angle 8.84799 / 6.29 ( 429) link_ALPHA1-2 : bond 0.00526 / 0.28 ( 1) link_ALPHA1-2 : angle 1.80415 / 0.92 ( 3) link_ALPHA1-3 : bond 0.00073 / 0.04 ( 1) link_ALPHA1-3 : angle 1.80432 / 0.93 ( 3) link_BETA1-4 : bond 0.00380 / 0.19 ( 2) link_BETA1-4 : angle 2.13839 / 1.08 ( 6) link_NAG-ASN : bond 0.02082 / 1.04 ( 4) link_NAG-ASN : angle 9.52468 / 5.53 ( 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 : 0.200 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: 0.5114 time to fit residues: 43.3987 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 : 0.194 ------------------------------------------------------------------------------- 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... 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 = 0.3521 r_free = 0.3521 target = 0.139564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109838 restraints weight = 4730.827| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.36 r_work: 0.3040 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 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 = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.0806 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= 0.128 Angle : 0.579 11.314 6882 Z= 0.303 Chirality : 0.048 0.486 761 Planarity : 0.004 0.043 876 Dihedral : 5.876 55.187 692 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.64 % Allowed : 15.44 % 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 are 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 A 224 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 0.001 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 5038) covalent geometry : angle 0.54903 / 0.30 ( 6836) SS BOND : bond 0.00226 / 0.17 ( 11) SS BOND : angle 0.58865 / 0.39 ( 22) hydrogen bonds : bond 0.03816 / 2.61 ( 160) hydrogen bonds : angle 6.82243 / 5.03 ( 429) link_ALPHA1-2 : bond 0.00675 / 0.36 ( 1) link_ALPHA1-2 : angle 1.63161 / 0.85 ( 3) link_ALPHA1-3 : bond 0.00376 / 0.20 ( 1) link_ALPHA1-3 : angle 1.39532 / 0.75 ( 3) link_BETA1-4 : bond 0.00374 / 0.18 ( 2) link_BETA1-4 : angle 1.60632 / 0.79 ( 6) link_NAG-ASN : bond 0.00696 / 0.35 ( 4) link_NAG-ASN : angle 4.18164 / 2.67 ( 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 89 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.191 Fit side-chains REVERT: L 100 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: A 277 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7952 (mt-10) REVERT: A 430 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7591 (mmt-90) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.5071 time to fit residues: 42.9721 Evaluate side-chains 76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3501 r_free = 0.3501 target = 0.137978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.109677 restraints weight = 4767.802| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.42 r_work: 0.2992 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5057 Z= 0.162 Angle : 0.586 11.520 6882 Z= 0.308 Chirality : 0.049 0.471 761 Planarity : 0.004 0.043 876 Dihedral : 5.466 46.202 686 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.20 % Allowed : 16.20 % Favored : 80.60 % 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 are not related in a simple way. whole: -0.21 (0.33), residues: 618 helix: 0.23 (2.37), residues: 6 sheet: -0.03 (0.31), residues: 232 loop : -0.13 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.013 0.002 TYR A 121 PHE 0.014 0.002 PHE A 354 TRP 0.014 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 5038) covalent geometry : angle 0.55682 / 0.30 ( 6836) SS BOND : bond 0.00253 / 0.20 ( 11) SS BOND : angle 0.63516 / 0.41 ( 22) hydrogen bonds : bond 0.03817 / 2.61 ( 160) hydrogen bonds : angle 6.47203 / 4.78 ( 429) link_ALPHA1-2 : bond 0.00626 / 0.33 ( 1) link_ALPHA1-2 : angle 1.67163 / 0.87 ( 3) link_ALPHA1-3 : bond 0.00248 / 0.13 ( 1) link_ALPHA1-3 : angle 1.56959 / 0.83 ( 3) link_BETA1-4 : bond 0.00331 / 0.16 ( 2) link_BETA1-4 : angle 1.70952 / 0.85 ( 6) link_NAG-ASN : bond 0.00912 / 0.46 ( 4) link_NAG-ASN : angle 4.10062 / 2.58 ( 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 88 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.117 Fit side-chains REVERT: A 277 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 368 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7587 (mt-10) outliers start: 17 outliers final: 10 residues processed: 80 average time/residue: 0.4985 time to fit residues: 41.7431 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 : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 MET 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: 0.6980 chunk 53 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3536 r_free = 0.3536 target = 0.140935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113528 restraints weight = 4753.994| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.37 r_work: 0.3050 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5057 Z= 0.114 Angle : 0.542 11.038 6882 Z= 0.283 Chirality : 0.047 0.464 761 Planarity : 0.004 0.043 876 Dihedral : 5.281 48.810 686 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.01 % Allowed : 16.20 % Favored : 80.79 % 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 are not related in a simple way. whole: -0.22 (0.33), residues: 618 helix: 0.28 (2.34), residues: 6 sheet: 0.01 (0.31), residues: 237 loop : -0.18 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.010 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 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5038) covalent geometry : angle 0.51377 / 0.28 ( 6836) SS BOND : bond 0.00159 / 0.12 ( 11) SS BOND : angle 0.48625 / 0.31 ( 22) hydrogen bonds : bond 0.03120 / 2.10 ( 160) hydrogen bonds : angle 6.14109 / 4.55 ( 429) link_ALPHA1-2 : bond 0.00686 / 0.36 ( 1) link_ALPHA1-2 : angle 1.50236 / 0.78 ( 3) link_ALPHA1-3 : bond 0.00518 / 0.27 ( 1) link_ALPHA1-3 : angle 1.35984 / 0.73 ( 3) link_BETA1-4 : bond 0.00447 / 0.22 ( 2) link_BETA1-4 : angle 1.51368 / 0.75 ( 6) link_NAG-ASN : bond 0.00908 / 0.45 ( 4) link_NAG-ASN : angle 3.90263 / 2.47 ( 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 90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.199 Fit side-chains REVERT: L 100 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: A 277 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8009 (mt-10) outliers start: 16 outliers final: 7 residues processed: 82 average time/residue: 0.5141 time to fit residues: 44.0838 Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 313 VAL 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: 4.9990 chunk 60 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN A 131 GLN A 402 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.106231 restraints weight = 4937.454| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.46 r_work: 0.2974 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5057 Z= 0.251 Angle : 0.652 11.553 6882 Z= 0.343 Chirality : 0.051 0.490 761 Planarity : 0.005 0.044 876 Dihedral : 5.831 48.124 686 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.58 % Allowed : 16.95 % 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 are not related in a simple way. whole: -0.37 (0.33), residues: 618 helix: 0.17 (2.38), residues: 6 sheet: -0.18 (0.31), residues: 224 loop : -0.22 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 38 TYR 0.016 0.002 TYR A 121 PHE 0.015 0.002 PHE A 354 TRP 0.012 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 ( 5038) covalent geometry : angle 0.62228 / 0.34 ( 6836) SS BOND : bond 0.00445 / 0.32 ( 11) SS BOND : angle 0.85436 / 0.55 ( 22) hydrogen bonds : bond 0.03958 / 2.70 ( 160) hydrogen bonds : angle 6.39786 / 4.76 ( 429) link_ALPHA1-2 : bond 0.00394 / 0.21 ( 1) link_ALPHA1-2 : angle 2.00040 / 1.02 ( 3) link_ALPHA1-3 : bond 0.00085 / 0.04 ( 1) link_ALPHA1-3 : angle 1.84281 / 0.97 ( 3) link_BETA1-4 : bond 0.00233 / 0.12 ( 2) link_BETA1-4 : angle 2.00696 / 1.00 ( 6) link_NAG-ASN : bond 0.00996 / 0.50 ( 4) link_NAG-ASN : angle 4.25241 / 2.65 ( 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 89 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.184 Fit side-chains REVERT: L 100 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7564 (pm20) REVERT: A 277 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8000 (mt-10) REVERT: A 368 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7594 (mt-10) outliers start: 19 outliers final: 12 residues processed: 82 average time/residue: 0.4820 time to fit residues: 41.3864 Evaluate side-chains 82 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 100 THR 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: 0.0870 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.109245 restraints weight = 4867.097| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.39 r_work: 0.3033 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5057 Z= 0.128 Angle : 0.560 11.127 6882 Z= 0.294 Chirality : 0.048 0.463 761 Planarity : 0.004 0.044 876 Dihedral : 5.472 49.925 686 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.64 % Allowed : 18.27 % 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 are not related in a simple way. whole: -0.28 (0.33), residues: 618 helix: 0.25 (2.38), residues: 6 sheet: -0.03 (0.32), residues: 232 loop : -0.22 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 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 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 5038) covalent geometry : angle 0.53079 / 0.29 ( 6836) SS BOND : bond 0.00234 / 0.17 ( 11) SS BOND : angle 0.79308 / 0.51 ( 22) hydrogen bonds : bond 0.03203 / 2.17 ( 160) hydrogen bonds : angle 6.09102 / 4.51 ( 429) link_ALPHA1-2 : bond 0.00704 / 0.37 ( 1) link_ALPHA1-2 : angle 1.58915 / 0.82 ( 3) link_ALPHA1-3 : bond 0.00483 / 0.25 ( 1) link_ALPHA1-3 : angle 1.36837 / 0.73 ( 3) link_BETA1-4 : bond 0.00427 / 0.21 ( 2) link_BETA1-4 : angle 1.62173 / 0.81 ( 6) link_NAG-ASN : bond 0.00905 / 0.45 ( 4) link_NAG-ASN : angle 3.95655 / 2.50 ( 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 84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.199 Fit side-chains REVERT: L 100 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: A 199 GLU cc_start: 0.7797 (pm20) cc_final: 0.7542 (mp0) REVERT: A 277 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7946 (mt-10) REVERT: A 308 LYS cc_start: 0.8452 (mtmp) cc_final: 0.8179 (mtmt) outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 0.5198 time to fit residues: 42.9871 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.135114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106506 restraints weight = 4782.571| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.42 r_work: 0.2951 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5057 Z= 0.252 Angle : 0.658 11.520 6882 Z= 0.344 Chirality : 0.051 0.486 761 Planarity : 0.005 0.044 876 Dihedral : 5.852 49.057 686 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.39 % Allowed : 17.70 % Favored : 78.91 % 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 are not related in a simple way. whole: -0.43 (0.32), residues: 618 helix: 0.16 (2.39), residues: 6 sheet: -0.22 (0.31), residues: 224 loop : -0.26 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.015 0.002 TYR A 121 PHE 0.014 0.002 PHE A 354 TRP 0.014 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 ( 5038) covalent geometry : angle 0.62711 / 0.34 ( 6836) SS BOND : bond 0.00459 / 0.38 ( 11) SS BOND : angle 1.20396 / 0.89 ( 22) hydrogen bonds : bond 0.03878 / 2.65 ( 160) hydrogen bonds : angle 6.31104 / 4.69 ( 429) link_ALPHA1-2 : bond 0.00460 / 0.24 ( 1) link_ALPHA1-2 : angle 1.99044 / 1.02 ( 3) link_ALPHA1-3 : bond 0.00081 / 0.04 ( 1) link_ALPHA1-3 : angle 1.75346 / 0.93 ( 3) link_BETA1-4 : bond 0.00157 / 0.08 ( 2) link_BETA1-4 : angle 1.97662 / 0.99 ( 6) link_NAG-ASN : bond 0.00969 / 0.48 ( 4) link_NAG-ASN : angle 4.22359 / 2.63 ( 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 90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.192 Fit side-chains REVERT: L 100 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: A 277 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 368 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: A 430 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7559 (mmt-90) outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 0.4925 time to fit residues: 42.3015 Evaluate side-chains 82 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 100 THR 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 Chi-restraints excluded: chain A residue 430 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.138875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110493 restraints weight = 4797.495| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.40 r_work: 0.3007 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1290 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= 0.135 Angle : 0.567 11.118 6882 Z= 0.298 Chirality : 0.048 0.464 761 Planarity : 0.004 0.044 876 Dihedral : 5.516 50.725 686 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.45 % Allowed : 19.02 % Favored : 78.53 % 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 are not related in a simple way. whole: -0.30 (0.33), residues: 618 helix: 0.35 (2.46), residues: 6 sheet: -0.03 (0.32), residues: 232 loop : -0.24 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.010 0.001 TYR A 121 PHE 0.013 0.001 PHE A 354 TRP 0.016 0.001 TRP A 178 HIS 0.002 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 5038) covalent geometry : angle 0.53722 / 0.29 ( 6836) SS BOND : bond 0.00235 / 0.20 ( 11) SS BOND : angle 0.92006 / 0.69 ( 22) hydrogen bonds : bond 0.03226 / 2.19 ( 160) hydrogen bonds : angle 6.05974 / 4.50 ( 429) link_ALPHA1-2 : bond 0.00685 / 0.36 ( 1) link_ALPHA1-2 : angle 1.62756 / 0.84 ( 3) link_ALPHA1-3 : bond 0.00450 / 0.24 ( 1) link_ALPHA1-3 : angle 1.37950 / 0.74 ( 3) link_BETA1-4 : bond 0.00437 / 0.22 ( 2) link_BETA1-4 : angle 1.66237 / 0.83 ( 6) link_NAG-ASN : bond 0.00911 / 0.46 ( 4) link_NAG-ASN : angle 3.95670 / 2.49 ( 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 85 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.191 Fit side-chains REVERT: L 100 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: A 277 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7938 (mt-10) REVERT: A 308 LYS cc_start: 0.8476 (mtmp) cc_final: 0.8268 (mtmt) outliers start: 13 outliers final: 10 residues processed: 80 average time/residue: 0.5141 time to fit residues: 43.1261 Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 LEU 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: 1.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109827 restraints weight = 4780.997| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.43 r_work: 0.3003 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5057 Z= 0.162 Angle : 0.591 11.230 6882 Z= 0.308 Chirality : 0.048 0.471 761 Planarity : 0.004 0.043 876 Dihedral : 5.551 50.907 686 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % 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 are not related in a simple way. whole: -0.35 (0.33), residues: 618 helix: 0.25 (2.39), residues: 6 sheet: -0.12 (0.32), residues: 226 loop : -0.24 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 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 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 5038) covalent geometry : angle 0.56143 / 0.30 ( 6836) SS BOND : bond 0.00292 / 0.24 ( 11) SS BOND : angle 0.92842 / 0.68 ( 22) hydrogen bonds : bond 0.03363 / 2.29 ( 160) hydrogen bonds : angle 6.05853 / 4.50 ( 429) link_ALPHA1-2 : bond 0.00583 / 0.31 ( 1) link_ALPHA1-2 : angle 1.73208 / 0.89 ( 3) link_ALPHA1-3 : bond 0.00260 / 0.14 ( 1) link_ALPHA1-3 : angle 1.54014 / 0.82 ( 3) link_BETA1-4 : bond 0.00366 / 0.18 ( 2) link_BETA1-4 : angle 1.74605 / 0.87 ( 6) link_NAG-ASN : bond 0.00916 / 0.46 ( 4) link_NAG-ASN : angle 4.00876 / 2.52 ( 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 84 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.198 Fit side-chains REVERT: L 100 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: A 277 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7974 (mt-10) outliers start: 12 outliers final: 9 residues processed: 80 average time/residue: 0.4955 time to fit residues: 41.4526 Evaluate side-chains 82 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.137203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.108829 restraints weight = 4796.571| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.43 r_work: 0.2987 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5057 Z= 0.185 Angle : 0.612 11.274 6882 Z= 0.319 Chirality : 0.049 0.475 761 Planarity : 0.004 0.045 876 Dihedral : 5.639 50.752 686 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % 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 are not related in a simple way. whole: -0.38 (0.33), residues: 618 helix: 0.23 (2.40), residues: 6 sheet: -0.15 (0.32), residues: 226 loop : -0.25 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 38 TYR 0.013 0.002 TYR A 121 PHE 0.013 0.002 PHE A 354 TRP 0.015 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 5038) covalent geometry : angle 0.58254 / 0.31 ( 6836) SS BOND : bond 0.00325 / 0.27 ( 11) SS BOND : angle 0.97020 / 0.70 ( 22) hydrogen bonds : bond 0.03480 / 2.36 ( 160) hydrogen bonds : angle 6.12083 / 4.55 ( 429) link_ALPHA1-2 : bond 0.00534 / 0.28 ( 1) link_ALPHA1-2 : angle 1.81495 / 0.93 ( 3) link_ALPHA1-3 : bond 0.00189 / 0.10 ( 1) link_ALPHA1-3 : angle 1.57549 / 0.84 ( 3) link_BETA1-4 : bond 0.00327 / 0.16 ( 2) link_BETA1-4 : angle 1.81579 / 0.91 ( 6) link_NAG-ASN : bond 0.00932 / 0.47 ( 4) link_NAG-ASN : angle 4.05218 / 2.54 ( 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: 12 poor density : 67 time to evaluate : 0.197 Fit side-chains REVERT: L 100 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: A 277 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8028 (mt-10) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.5874 time to fit residues: 45.2762 Evaluate side-chains 76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3498 r_free = 0.3498 target = 0.137688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109395 restraints weight = 4797.771| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.42 r_work: 0.2996 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5057 Z= 0.168 Angle : 0.597 11.190 6882 Z= 0.313 Chirality : 0.049 0.472 761 Planarity : 0.004 0.044 876 Dihedral : 5.591 50.865 686 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.07 % Allowed : 19.59 % Favored : 78.34 % 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 are not related in a simple way. whole: -0.38 (0.33), residues: 618 helix: 0.25 (2.40), residues: 6 sheet: -0.14 (0.32), residues: 226 loop : -0.25 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 61 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 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 5038) covalent geometry : angle 0.56806 / 0.31 ( 6836) SS BOND : bond 0.00292 / 0.24 ( 11) SS BOND : angle 0.91289 / 0.66 ( 22) hydrogen bonds : bond 0.03401 / 2.31 ( 160) hydrogen bonds : angle 6.07895 / 4.51 ( 429) link_ALPHA1-2 : bond 0.00569 / 0.30 ( 1) link_ALPHA1-2 : angle 1.77302 / 0.91 ( 3) link_ALPHA1-3 : bond 0.00250 / 0.13 ( 1) link_ALPHA1-3 : angle 1.52087 / 0.81 ( 3) link_BETA1-4 : bond 0.00357 / 0.18 ( 2) link_BETA1-4 : angle 1.78412 / 0.89 ( 6) link_NAG-ASN : bond 0.00918 / 0.46 ( 4) link_NAG-ASN : angle 4.01368 / 2.52 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.59 seconds wall clock time: 38 minutes 35.90 seconds (2315.90 seconds total)