Starting phenix.real_space_refine on Thu Jul 2 01:03:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez8_28730/07_2026/8ez8_28730.cif" } resolution = 2.78 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= 0.002 sd= 0.068 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 2997 2.51 5 N 838 2.21 5 O 984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 4847 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 951 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 786 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} 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: 0.91, per 1000 atoms: 0.19 Number of scatterers: 4847 At special positions: 0 Unit cell: (76.32, 96.46, 92.22, 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 984 8.00 N 838 7.00 C 2997 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=2.02 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=2.03 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=2.04 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 234 " " NAG A 504 " - " ASN A 329 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 172.7 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1106 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 4.2% alpha, 41.1% 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 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.007A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.637A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.664A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.573A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.252A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.884A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.884A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 16 through 24 removed outlier: 4.127A pdb=" N GLN L 17 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY L 77 " --> pdb=" O GLN L 17 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.587A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.619A 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 125 removed outlier: 4.647A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.583A 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: 3.566A pdb=" N SER A 179 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.751A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR A 252 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 254 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 279 through 283 Processing sheet with id=AB2, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.703A 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: 6.857A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 414 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: 0.75 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1593 1.35 - 1.47: 1277 1.47 - 1.59: 2051 1.59 - 1.71: 0 1.71 - 1.83: 34 Bond restraints: 4955 Sorted by residual: bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.56e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.448 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.446 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 4950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 6459 1.35 - 2.69: 207 2.69 - 4.04: 46 4.04 - 5.38: 11 5.38 - 6.73: 6 Bond angle restraints: 6729 Sorted by residual: angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.88 -5.18 1.80e+00 3.09e-01 8.29e+00 angle pdb=" CA CYS A 230 " pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " ideal model delta sigma weight residual 114.40 120.11 -5.71 2.30e+00 1.89e-01 6.16e+00 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 122.07 125.45 -3.38 1.43e+00 4.89e-01 5.59e+00 angle pdb=" C SER L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 105.25 6.52 3.00e+00 1.11e-01 4.72e+00 ... (remaining 6724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2454 17.46 - 34.92: 321 34.92 - 52.39: 76 52.39 - 69.85: 11 69.85 - 87.31: 9 Dihedral angle restraints: 2871 sinusoidal: 1126 harmonic: 1745 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+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 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 2868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 592 0.053 - 0.105: 123 0.105 - 0.158: 35 0.158 - 0.210: 2 0.210 - 0.263: 1 Chirality restraints: 753 Sorted by residual: 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 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" C2 MAN B 4 " pdb=" C1 MAN B 4 " pdb=" C3 MAN B 4 " pdb=" O2 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.52 2.67 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 750 not shown) Planarity restraints: 866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO L 8 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 78 " -0.010 2.00e-02 2.50e+03 7.48e-03 9.80e-01 pdb=" CG PHE H 78 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE H 78 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE H 78 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE H 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 78 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 78 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN H 39 " 0.005 2.00e-02 2.50e+03 9.72e-03 9.44e-01 pdb=" C GLN H 39 " -0.017 2.00e-02 2.50e+03 pdb=" O GLN H 39 " 0.006 2.00e-02 2.50e+03 pdb=" N PRO H 40 " 0.006 2.00e-02 2.50e+03 ... (remaining 863 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 50 2.53 - 3.13: 3649 3.13 - 3.72: 7634 3.72 - 4.31: 11502 4.31 - 4.90: 19416 Nonbonded interactions: 42251 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 1.943 3.120 nonbonded pdb=" CZ ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.202 3.270 nonbonded pdb=" O VAL A 317 " pdb=" OG SER A 335 " model vdw 2.245 3.040 nonbonded pdb=" OG SER A 279 " pdb=" O GLY A 351 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 121 " pdb=" OG SER A 182 " model vdw 2.258 3.040 ... (remaining 42246 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.020 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 0.033 4974 Z= 0.168 Angle : 0.636 6.728 6775 Z= 0.321 Chirality : 0.048 0.263 753 Planarity : 0.003 0.050 862 Dihedral : 16.488 87.309 1732 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 1.89 % Allowed : 26.65 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.51 (0.35), residues: 615 helix: -1.81 (1.45), residues: 12 sheet: 0.00 (0.34), residues: 226 loop : -0.45 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 43 TYR 0.013 0.001 TYR A 121 PHE 0.017 0.002 PHE H 78 TRP 0.013 0.001 TRP H 34 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 4955) covalent geometry : angle 0.62121 / 0.32 ( 6729) SS BOND : bond 0.00306 / 0.18 ( 11) SS BOND : angle 1.48614 / 0.93 ( 22) hydrogen bonds : bond 0.12395 / 8.83 ( 152) hydrogen bonds : angle 7.95801 / 5.53 ( 414) link_ALPHA1-2 : bond 0.00452 / 0.24 ( 1) link_ALPHA1-2 : angle 1.88553 / 0.92 ( 3) link_ALPHA1-3 : bond 0.00545 / 0.29 ( 1) link_ALPHA1-3 : angle 1.15005 / 0.60 ( 3) link_BETA1-4 : bond 0.00468 / 0.23 ( 2) link_BETA1-4 : angle 1.93335 / 0.96 ( 6) link_NAG-ASN : bond 0.00270 / 0.13 ( 4) link_NAG-ASN : angle 2.19548 / 1.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.190 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.4154 time to fit residues: 35.0181 Evaluate side-chains 79 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** 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 = 0.3524 r_free = 0.3524 target = 0.114381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092360 restraints weight = 6409.524| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.06 r_work: 0.3123 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4974 Z= 0.137 Angle : 0.543 7.457 6775 Z= 0.287 Chirality : 0.046 0.158 753 Planarity : 0.004 0.045 862 Dihedral : 5.563 59.573 682 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 3.02 % Allowed : 25.90 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.48 (0.35), residues: 615 helix: -1.69 (1.49), residues: 12 sheet: 0.00 (0.35), residues: 220 loop : -0.41 (0.34), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 85 TYR 0.011 0.001 TYR A 121 PHE 0.015 0.002 PHE H 78 TRP 0.014 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 4955) covalent geometry : angle 0.52987 / 0.28 ( 6729) SS BOND : bond 0.00198 / 0.13 ( 11) SS BOND : angle 0.92735 / 0.58 ( 22) hydrogen bonds : bond 0.02934 / 2.00 ( 152) hydrogen bonds : angle 6.64239 / 4.63 ( 414) link_ALPHA1-2 : bond 0.00534 / 0.28 ( 1) link_ALPHA1-2 : angle 1.71249 / 0.84 ( 3) link_ALPHA1-3 : bond 0.00598 / 0.31 ( 1) link_ALPHA1-3 : angle 1.53727 / 0.85 ( 3) link_BETA1-4 : bond 0.00395 / 0.20 ( 2) link_BETA1-4 : angle 1.69514 / 0.80 ( 6) link_NAG-ASN : bond 0.00202 / 0.10 ( 4) link_NAG-ASN : angle 2.11128 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 431 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7750 (tppt) outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 0.4005 time to fit residues: 35.9670 Evaluate side-chains 77 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN A 136 GLN A 264 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.087381 restraints weight = 6509.111| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.05 r_work: 0.3071 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4974 Z= 0.310 Angle : 0.652 6.824 6775 Z= 0.340 Chirality : 0.049 0.166 753 Planarity : 0.004 0.041 862 Dihedral : 5.415 46.919 673 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 4.16 % Allowed : 23.44 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.84 (0.34), residues: 615 helix: -1.73 (1.50), residues: 12 sheet: -0.46 (0.33), residues: 236 loop : -0.51 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 420 TYR 0.016 0.002 TYR L 36 PHE 0.019 0.003 PHE H 78 TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00697 / 0.31 ( 4955) covalent geometry : angle 0.63362 / 0.34 ( 6729) SS BOND : bond 0.00420 / 0.26 ( 11) SS BOND : angle 1.21504 / 0.74 ( 22) hydrogen bonds : bond 0.03488 / 2.37 ( 152) hydrogen bonds : angle 6.69583 / 4.73 ( 414) link_ALPHA1-2 : bond 0.00127 / 0.07 ( 1) link_ALPHA1-2 : angle 2.12804 / 1.03 ( 3) link_ALPHA1-3 : bond 0.00204 / 0.11 ( 1) link_ALPHA1-3 : angle 1.84826 / 1.03 ( 3) link_BETA1-4 : bond 0.00193 / 0.10 ( 2) link_BETA1-4 : angle 2.29344 / 1.13 ( 6) link_NAG-ASN : bond 0.00404 / 0.19 ( 4) link_NAG-ASN : angle 2.81493 / 1.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: H 102 ILE cc_start: 0.8403 (mm) cc_final: 0.8181 (tp) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.4414 time to fit residues: 39.1176 Evaluate side-chains 85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089905 restraints weight = 6377.763| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.06 r_work: 0.3086 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4974 Z= 0.178 Angle : 0.565 6.046 6775 Z= 0.297 Chirality : 0.046 0.167 753 Planarity : 0.004 0.041 862 Dihedral : 5.190 47.960 673 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 4.54 % Allowed : 24.01 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.70 (0.34), residues: 615 helix: -1.75 (1.45), residues: 12 sheet: -0.27 (0.32), residues: 240 loop : -0.48 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 43 TYR 0.012 0.001 TYR A 121 PHE 0.019 0.002 PHE H 78 TRP 0.014 0.002 TRP H 47 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 4955) covalent geometry : angle 0.55093 / 0.29 ( 6729) SS BOND : bond 0.00236 / 0.16 ( 11) SS BOND : angle 0.91259 / 0.56 ( 22) hydrogen bonds : bond 0.02997 / 2.06 ( 152) hydrogen bonds : angle 6.42637 / 4.52 ( 414) link_ALPHA1-2 : bond 0.00330 / 0.17 ( 1) link_ALPHA1-2 : angle 1.87106 / 0.91 ( 3) link_ALPHA1-3 : bond 0.00546 / 0.29 ( 1) link_ALPHA1-3 : angle 1.44330 / 0.81 ( 3) link_BETA1-4 : bond 0.00413 / 0.21 ( 2) link_BETA1-4 : angle 1.89679 / 0.94 ( 6) link_NAG-ASN : bond 0.00232 / 0.11 ( 4) link_NAG-ASN : angle 2.35057 / 1.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 ILE cc_start: 0.8405 (mm) cc_final: 0.8201 (tp) outliers start: 24 outliers final: 14 residues processed: 93 average time/residue: 0.3759 time to fit residues: 36.8577 Evaluate side-chains 84 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN A 441 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090068 restraints weight = 6454.980| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.06 r_work: 0.3087 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4974 Z= 0.183 Angle : 0.569 8.272 6775 Z= 0.296 Chirality : 0.046 0.166 753 Planarity : 0.003 0.039 862 Dihedral : 5.179 48.224 673 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 5.29 % Allowed : 24.01 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.67 (0.34), residues: 615 helix: -0.19 (2.39), residues: 6 sheet: -0.16 (0.32), residues: 239 loop : -0.59 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 43 TYR 0.013 0.001 TYR L 36 PHE 0.018 0.002 PHE H 78 TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 4955) covalent geometry : angle 0.55527 / 0.29 ( 6729) SS BOND : bond 0.00254 / 0.16 ( 11) SS BOND : angle 0.84322 / 0.52 ( 22) hydrogen bonds : bond 0.02977 / 2.04 ( 152) hydrogen bonds : angle 6.36665 / 4.49 ( 414) link_ALPHA1-2 : bond 0.00283 / 0.15 ( 1) link_ALPHA1-2 : angle 1.87190 / 0.91 ( 3) link_ALPHA1-3 : bond 0.00508 / 0.27 ( 1) link_ALPHA1-3 : angle 1.46399 / 0.81 ( 3) link_BETA1-4 : bond 0.00355 / 0.18 ( 2) link_BETA1-4 : angle 1.90383 / 0.93 ( 6) link_NAG-ASN : bond 0.00240 / 0.11 ( 4) link_NAG-ASN : angle 2.29740 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 ILE cc_start: 0.8406 (mm) cc_final: 0.8194 (tp) outliers start: 28 outliers final: 20 residues processed: 92 average time/residue: 0.4083 time to fit residues: 39.5600 Evaluate side-chains 90 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.114105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091545 restraints weight = 6456.663| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.10 r_work: 0.3112 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4974 Z= 0.140 Angle : 0.540 6.430 6775 Z= 0.283 Chirality : 0.045 0.164 753 Planarity : 0.003 0.038 862 Dihedral : 5.078 48.944 673 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.74 % Favored : 96.10 % Rotamer: Outliers : 3.97 % Allowed : 25.33 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.60 (0.35), residues: 615 helix: -0.11 (2.38), residues: 6 sheet: -0.20 (0.32), residues: 237 loop : -0.48 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 43 TYR 0.011 0.001 TYR A 121 PHE 0.018 0.002 PHE H 78 TRP 0.012 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4955) covalent geometry : angle 0.52821 / 0.28 ( 6729) SS BOND : bond 0.00213 / 0.13 ( 11) SS BOND : angle 0.82865 / 0.50 ( 22) hydrogen bonds : bond 0.02826 / 1.95 ( 152) hydrogen bonds : angle 6.20310 / 4.37 ( 414) link_ALPHA1-2 : bond 0.00393 / 0.21 ( 1) link_ALPHA1-2 : angle 1.76858 / 0.86 ( 3) link_ALPHA1-3 : bond 0.00621 / 0.33 ( 1) link_ALPHA1-3 : angle 1.32088 / 0.73 ( 3) link_BETA1-4 : bond 0.00427 / 0.21 ( 2) link_BETA1-4 : angle 1.78621 / 0.87 ( 6) link_NAG-ASN : bond 0.00173 / 0.08 ( 4) link_NAG-ASN : angle 2.06847 / 1.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 ILE cc_start: 0.8403 (mm) cc_final: 0.8201 (tp) outliers start: 21 outliers final: 15 residues processed: 92 average time/residue: 0.4220 time to fit residues: 40.8586 Evaluate side-chains 83 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090617 restraints weight = 6456.148| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.06 r_work: 0.3098 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4974 Z= 0.180 Angle : 0.574 8.839 6775 Z= 0.299 Chirality : 0.046 0.164 753 Planarity : 0.003 0.038 862 Dihedral : 5.131 48.995 673 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 4.16 % Allowed : 26.09 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.65 (0.35), residues: 615 helix: -0.24 (2.35), residues: 6 sheet: -0.20 (0.32), residues: 241 loop : -0.53 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 43 TYR 0.014 0.001 TYR L 36 PHE 0.017 0.002 PHE H 78 TRP 0.012 0.001 TRP H 34 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 4955) covalent geometry : angle 0.55995 / 0.30 ( 6729) SS BOND : bond 0.00304 / 0.18 ( 11) SS BOND : angle 1.06882 / 0.63 ( 22) hydrogen bonds : bond 0.02940 / 2.01 ( 152) hydrogen bonds : angle 6.25694 / 4.42 ( 414) link_ALPHA1-2 : bond 0.00279 / 0.15 ( 1) link_ALPHA1-2 : angle 1.85174 / 0.90 ( 3) link_ALPHA1-3 : bond 0.00486 / 0.26 ( 1) link_ALPHA1-3 : angle 1.43642 / 0.79 ( 3) link_BETA1-4 : bond 0.00342 / 0.17 ( 2) link_BETA1-4 : angle 1.87592 / 0.91 ( 6) link_NAG-ASN : bond 0.00227 / 0.11 ( 4) link_NAG-ASN : angle 2.18416 / 1.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7359 (mtm-85) REVERT: H 102 ILE cc_start: 0.8407 (mm) cc_final: 0.8191 (tp) REVERT: A 128 LYS cc_start: 0.8006 (ptpp) cc_final: 0.7197 (ptmt) REVERT: A 162 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7656 (mm-30) outliers start: 22 outliers final: 18 residues processed: 88 average time/residue: 0.4619 time to fit residues: 42.5897 Evaluate side-chains 90 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091906 restraints weight = 6477.448| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.08 r_work: 0.3113 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4974 Z= 0.140 Angle : 0.547 6.857 6775 Z= 0.286 Chirality : 0.045 0.166 753 Planarity : 0.003 0.037 862 Dihedral : 5.063 49.772 673 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 4.35 % Allowed : 25.90 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.35), residues: 615 helix: -0.12 (2.38), residues: 6 sheet: -0.13 (0.32), residues: 236 loop : -0.45 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 43 TYR 0.010 0.001 TYR A 121 PHE 0.017 0.002 PHE H 78 TRP 0.013 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4955) covalent geometry : angle 0.53469 / 0.28 ( 6729) SS BOND : bond 0.00262 / 0.15 ( 11) SS BOND : angle 0.87987 / 0.53 ( 22) hydrogen bonds : bond 0.02789 / 1.92 ( 152) hydrogen bonds : angle 6.18122 / 4.35 ( 414) link_ALPHA1-2 : bond 0.00385 / 0.20 ( 1) link_ALPHA1-2 : angle 1.75656 / 0.86 ( 3) link_ALPHA1-3 : bond 0.00620 / 0.33 ( 1) link_ALPHA1-3 : angle 1.29673 / 0.71 ( 3) link_BETA1-4 : bond 0.00386 / 0.19 ( 2) link_BETA1-4 : angle 1.81349 / 0.88 ( 6) link_NAG-ASN : bond 0.00170 / 0.08 ( 4) link_NAG-ASN : angle 2.01201 / 1.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7381 (mtm-85) REVERT: H 102 ILE cc_start: 0.8417 (mm) cc_final: 0.8198 (tp) REVERT: A 407 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8577 (t) outliers start: 23 outliers final: 15 residues processed: 92 average time/residue: 0.4511 time to fit residues: 43.5735 Evaluate side-chains 87 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091198 restraints weight = 6385.705| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.07 r_work: 0.3105 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4974 Z= 0.176 Angle : 0.575 9.121 6775 Z= 0.299 Chirality : 0.046 0.165 753 Planarity : 0.004 0.036 862 Dihedral : 5.139 49.471 673 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.55 % Favored : 95.28 % Rotamer: Outliers : 3.78 % Allowed : 26.84 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.58 (0.34), residues: 615 helix: -0.26 (2.35), residues: 6 sheet: -0.09 (0.32), residues: 239 loop : -0.54 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 103 TYR 0.013 0.001 TYR L 36 PHE 0.016 0.002 PHE H 78 TRP 0.012 0.001 TRP H 34 HIS 0.003 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 4955) covalent geometry : angle 0.56218 / 0.30 ( 6729) SS BOND : bond 0.00285 / 0.17 ( 11) SS BOND : angle 0.96362 / 0.57 ( 22) hydrogen bonds : bond 0.02885 / 1.97 ( 152) hydrogen bonds : angle 6.22479 / 4.39 ( 414) link_ALPHA1-2 : bond 0.00279 / 0.15 ( 1) link_ALPHA1-2 : angle 1.83495 / 0.89 ( 3) link_ALPHA1-3 : bond 0.00505 / 0.27 ( 1) link_ALPHA1-3 : angle 1.40544 / 0.77 ( 3) link_BETA1-4 : bond 0.00340 / 0.17 ( 2) link_BETA1-4 : angle 1.88718 / 0.92 ( 6) link_NAG-ASN : bond 0.00211 / 0.10 ( 4) link_NAG-ASN : angle 2.13076 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 95 ASP cc_start: 0.8124 (t0) cc_final: 0.7775 (t0) REVERT: H 100 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7346 (mtm-85) REVERT: H 102 ILE cc_start: 0.8428 (mm) cc_final: 0.8201 (tp) REVERT: A 128 LYS cc_start: 0.7836 (ptpp) cc_final: 0.7208 (ptmt) REVERT: A 162 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 407 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8583 (t) outliers start: 20 outliers final: 18 residues processed: 89 average time/residue: 0.4602 time to fit residues: 43.0271 Evaluate side-chains 92 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.093253 restraints weight = 6408.750| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.07 r_work: 0.3138 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4974 Z= 0.116 Angle : 0.531 6.694 6775 Z= 0.279 Chirality : 0.045 0.165 753 Planarity : 0.003 0.036 862 Dihedral : 4.939 49.979 673 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.42 % Rotamer: Outliers : 3.21 % Allowed : 27.60 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.50 (0.35), residues: 615 helix: -0.02 (2.38), residues: 6 sheet: -0.14 (0.33), residues: 240 loop : -0.41 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 43 TYR 0.011 0.001 TYR L 49 PHE 0.017 0.002 PHE H 78 TRP 0.013 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 4955) covalent geometry : angle 0.52155 / 0.28 ( 6729) SS BOND : bond 0.00200 / 0.11 ( 11) SS BOND : angle 0.78163 / 0.47 ( 22) hydrogen bonds : bond 0.02670 / 1.83 ( 152) hydrogen bonds : angle 6.06034 / 4.26 ( 414) link_ALPHA1-2 : bond 0.00399 / 0.21 ( 1) link_ALPHA1-2 : angle 1.62659 / 0.80 ( 3) link_ALPHA1-3 : bond 0.00743 / 0.39 ( 1) link_ALPHA1-3 : angle 1.25337 / 0.68 ( 3) link_BETA1-4 : bond 0.00427 / 0.21 ( 2) link_BETA1-4 : angle 1.68709 / 0.82 ( 6) link_NAG-ASN : bond 0.00142 / 0.07 ( 4) link_NAG-ASN : angle 1.81404 / 1.00 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 81 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7717 (mmm-85) REVERT: H 95 ASP cc_start: 0.8160 (t0) cc_final: 0.7758 (t0) REVERT: H 100 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7353 (mtm-85) REVERT: H 102 ILE cc_start: 0.8440 (mm) cc_final: 0.8232 (tp) REVERT: A 128 LYS cc_start: 0.7742 (ptpp) cc_final: 0.7059 (ptmt) REVERT: A 162 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 407 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8526 (t) REVERT: A 466 LEU cc_start: 0.8269 (mt) cc_final: 0.8010 (mp) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.4806 time to fit residues: 45.4031 Evaluate side-chains 85 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 407 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.0050 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN L 37 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093287 restraints weight = 6415.168| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.08 r_work: 0.3143 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4974 Z= 0.117 Angle : 0.533 9.054 6775 Z= 0.278 Chirality : 0.045 0.163 753 Planarity : 0.003 0.036 862 Dihedral : 4.826 50.635 672 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.90 % Favored : 95.93 % Rotamer: Outliers : 2.46 % Allowed : 27.98 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.35), residues: 615 helix: 0.14 (2.42), residues: 6 sheet: -0.03 (0.33), residues: 233 loop : -0.42 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 43 TYR 0.010 0.001 TYR L 36 PHE 0.016 0.002 PHE H 78 TRP 0.013 0.001 TRP H 34 HIS 0.002 0.001 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 4955) covalent geometry : angle 0.52345 / 0.28 ( 6729) SS BOND : bond 0.00231 / 0.13 ( 11) SS BOND : angle 0.77597 / 0.46 ( 22) hydrogen bonds : bond 0.02649 / 1.81 ( 152) hydrogen bonds : angle 6.00895 / 4.23 ( 414) link_ALPHA1-2 : bond 0.00467 / 0.25 ( 1) link_ALPHA1-2 : angle 1.68559 / 0.82 ( 3) link_ALPHA1-3 : bond 0.00615 / 0.32 ( 1) link_ALPHA1-3 : angle 1.26772 / 0.68 ( 3) link_BETA1-4 : bond 0.00428 / 0.21 ( 2) link_BETA1-4 : angle 1.67969 / 0.81 ( 6) link_NAG-ASN : bond 0.00153 / 0.08 ( 4) link_NAG-ASN : angle 1.79721 / 0.98 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.83 seconds wall clock time: 51 minutes 11.14 seconds (3071.14 seconds total)