Starting phenix.real_space_refine on Wed Sep 17 04:15:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c45_45175/09_2025/9c45_45175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c45_45175/09_2025/9c45_45175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c45_45175/09_2025/9c45_45175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c45_45175/09_2025/9c45_45175.map" model { file = "/net/cci-nas-00/data/ceres_data/9c45_45175/09_2025/9c45_45175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c45_45175/09_2025/9c45_45175.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.085 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 14 5.16 5 C 2530 2.51 5 N 642 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3900 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 806 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2048 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 4 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.22, per 1000 atoms: 0.31 Number of scatterers: 3900 At special positions: 0 Unit cell: (91.044, 69.126, 80.928, 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 14 16.00 O 714 8.00 N 642 7.00 C 2530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 165 " " NAG B 1 " - " ASN A 122 " " NAG C 1 " - " ASN A 234 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 150.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 11 sheets defined 5.4% alpha, 50.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 294 through 304 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.042A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.652A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.766A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.766A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.425A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.276A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 153 through 155 167 hydrogen bonds defined for protein. 402 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: 0.53 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 847 1.33 - 1.45: 978 1.45 - 1.57: 2159 1.57 - 1.70: 1 1.70 - 1.82: 18 Bond restraints: 4003 Sorted by residual: bond pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " ideal model delta sigma weight residual 1.530 1.587 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.66e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.466 -0.053 2.00e-02 2.50e+03 7.09e+00 ... (remaining 3998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4637 1.56 - 3.12: 677 3.12 - 4.68: 79 4.68 - 6.25: 48 6.25 - 7.81: 18 Bond angle restraints: 5459 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.00 -6.34 7.20e-01 1.93e+00 7.76e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.63 -7.60 9.90e-01 1.02e+00 5.89e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.85 127.30 -7.45 1.01e+00 9.80e-01 5.45e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.07 -7.22 1.01e+00 9.80e-01 5.11e+01 angle pdb=" C GLY L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta sigma weight residual 119.32 127.13 -7.81 1.14e+00 7.69e-01 4.69e+01 ... (remaining 5454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 2351 21.34 - 42.68: 53 42.68 - 64.02: 9 64.02 - 85.36: 7 85.36 - 106.70: 4 Dihedral angle restraints: 2424 sinusoidal: 984 harmonic: 1440 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.61 45.39 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ASP A 138 " pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.99 106.70 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 2421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 456 0.071 - 0.143: 122 0.143 - 0.214: 35 0.214 - 0.285: 3 0.285 - 0.356: 8 Chirality restraints: 624 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 3.17e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.89e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.86e+01 ... (remaining 621 not shown) Planarity restraints: 697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 31 " 0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C PHE L 31 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE L 31 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR L 32 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 122 " -0.028 2.00e-02 2.50e+03 2.88e-02 1.04e+01 pdb=" CG ASN A 122 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 122 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 122 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.63e+00 pdb=" CG TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.010 2.00e-02 2.50e+03 ... (remaining 694 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1953 2.99 - 3.46: 3208 3.46 - 3.94: 6396 3.94 - 4.42: 7253 4.42 - 4.90: 12349 Nonbonded interactions: 31159 Sorted by model distance: nonbonded pdb=" O THR H 28 " pdb=" CG2 THR H 28 " model vdw 2.507 3.460 nonbonded pdb=" N ASP A 138 " pdb=" OD1 ASP A 138 " model vdw 2.573 3.120 nonbonded pdb=" N ARG A 158 " pdb=" N VAL A 159 " model vdw 2.574 2.560 nonbonded pdb=" N PHE H 27 " pdb=" O PHE H 27 " model vdw 2.602 2.496 nonbonded pdb=" OG1 THR A 108 " pdb=" N THR A 109 " model vdw 2.607 3.120 ... (remaining 31154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.380 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.950 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.011 0.060 4017 Z= 0.597 Angle : 1.272 7.808 5496 Z= 0.838 Chirality : 0.078 0.356 624 Planarity : 0.005 0.040 691 Dihedral : 11.880 106.704 1487 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.38), residues: 482 helix: 0.89 (1.63), residues: 11 sheet: 1.24 (0.35), residues: 215 loop : 0.87 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 103 TYR 0.025 0.004 TYR A 269 PHE 0.016 0.003 PHE A 55 TRP 0.024 0.004 TRP H 47 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.01092 ( 4003) covalent geometry : angle 1.25623 ( 5459) SS BOND : bond 0.00737 ( 5) SS BOND : angle 3.65067 ( 10) hydrogen bonds : bond 0.14217 ( 155) hydrogen bonds : angle 8.54372 ( 402) link_BETA1-4 : bond 0.05693 ( 3) link_BETA1-4 : angle 2.69629 ( 9) link_NAG-ASN : bond 0.05533 ( 6) link_NAG-ASN : angle 2.07045 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.8751 (m-80) cc_final: 0.8448 (m-80) REVERT: A 202 LYS cc_start: 0.8586 (mttm) cc_final: 0.8355 (mttp) REVERT: A 280 ASN cc_start: 0.8658 (p0) cc_final: 0.8088 (p0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0971 time to fit residues: 6.0255 Evaluate side-chains 40 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107817 restraints weight = 4286.930| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.37 r_work: 0.2991 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4017 Z= 0.148 Angle : 0.631 12.851 5496 Z= 0.312 Chirality : 0.046 0.159 624 Planarity : 0.004 0.031 691 Dihedral : 9.007 72.154 723 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.84 % Allowed : 3.65 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.39), residues: 482 helix: 2.76 (1.71), residues: 11 sheet: 1.32 (0.35), residues: 218 loop : 0.89 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.017 0.001 TYR A 170 PHE 0.012 0.001 PHE H 50 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4003) covalent geometry : angle 0.56523 ( 5459) SS BOND : bond 0.00304 ( 5) SS BOND : angle 0.93317 ( 10) hydrogen bonds : bond 0.03556 ( 155) hydrogen bonds : angle 6.44150 ( 402) link_BETA1-4 : bond 0.00612 ( 3) link_BETA1-4 : angle 2.14668 ( 9) link_NAG-ASN : bond 0.00625 ( 6) link_NAG-ASN : angle 4.69882 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: A 62 VAL cc_start: 0.9063 (t) cc_final: 0.8831 (m) REVERT: A 202 LYS cc_start: 0.8644 (mttm) cc_final: 0.8353 (mttp) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.0752 time to fit residues: 4.0093 Evaluate side-chains 37 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.095374 restraints weight = 4337.878| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.33 r_work: 0.2807 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4017 Z= 0.226 Angle : 0.644 12.932 5496 Z= 0.318 Chirality : 0.048 0.154 624 Planarity : 0.004 0.031 691 Dihedral : 6.615 46.186 723 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.40 % Allowed : 4.49 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.38), residues: 482 helix: 2.71 (1.64), residues: 11 sheet: 1.14 (0.36), residues: 201 loop : 0.38 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 38 TYR 0.018 0.002 TYR A 170 PHE 0.018 0.002 PHE H 50 TRP 0.018 0.002 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 4003) covalent geometry : angle 0.59959 ( 5459) SS BOND : bond 0.00346 ( 5) SS BOND : angle 0.82601 ( 10) hydrogen bonds : bond 0.03516 ( 155) hydrogen bonds : angle 5.88729 ( 402) link_BETA1-4 : bond 0.00472 ( 3) link_BETA1-4 : angle 2.10160 ( 9) link_NAG-ASN : bond 0.00214 ( 6) link_NAG-ASN : angle 3.86333 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8804 (mttm) cc_final: 0.8467 (mttp) REVERT: A 215 ASP cc_start: 0.7978 (p0) cc_final: 0.7732 (p0) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.0962 time to fit residues: 5.7751 Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 25 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.105453 restraints weight = 4211.754| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.35 r_work: 0.2947 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4017 Z= 0.143 Angle : 0.543 10.187 5496 Z= 0.270 Chirality : 0.044 0.146 624 Planarity : 0.004 0.031 691 Dihedral : 5.167 39.070 723 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.12 % Allowed : 5.90 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.38), residues: 482 helix: 2.53 (1.59), residues: 11 sheet: 1.05 (0.36), residues: 201 loop : 0.33 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.017 0.001 TYR A 170 PHE 0.012 0.001 PHE H 50 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4003) covalent geometry : angle 0.50705 ( 5459) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.50638 ( 10) hydrogen bonds : bond 0.02932 ( 155) hydrogen bonds : angle 5.68761 ( 402) link_BETA1-4 : bond 0.00416 ( 3) link_BETA1-4 : angle 1.85816 ( 9) link_NAG-ASN : bond 0.00330 ( 6) link_NAG-ASN : angle 3.20228 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7954 (p0) cc_final: 0.7743 (p0) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.0949 time to fit residues: 4.8878 Evaluate side-chains 40 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.097432 restraints weight = 4326.449| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.31 r_work: 0.2830 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4017 Z= 0.237 Angle : 0.602 9.976 5496 Z= 0.298 Chirality : 0.046 0.159 624 Planarity : 0.004 0.030 691 Dihedral : 4.975 29.642 723 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.97 % Allowed : 6.18 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.38), residues: 482 helix: 2.80 (1.63), residues: 11 sheet: 0.87 (0.36), residues: 201 loop : 0.21 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.015 0.002 TYR A 170 PHE 0.016 0.002 PHE H 50 TRP 0.016 0.002 TRP H 47 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 4003) covalent geometry : angle 0.57313 ( 5459) SS BOND : bond 0.00368 ( 5) SS BOND : angle 0.72654 ( 10) hydrogen bonds : bond 0.03235 ( 155) hydrogen bonds : angle 5.78851 ( 402) link_BETA1-4 : bond 0.00353 ( 3) link_BETA1-4 : angle 1.74810 ( 9) link_NAG-ASN : bond 0.00316 ( 6) link_NAG-ASN : angle 3.01032 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8404 (tt0) cc_final: 0.8137 (tt0) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.0991 time to fit residues: 4.8197 Evaluate side-chains 41 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.134876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103358 restraints weight = 4254.261| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.25 r_work: 0.2865 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4017 Z= 0.196 Angle : 0.563 10.299 5496 Z= 0.280 Chirality : 0.045 0.146 624 Planarity : 0.004 0.030 691 Dihedral : 4.707 20.621 723 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.25 % Allowed : 6.18 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.38), residues: 482 helix: -0.20 (1.43), residues: 17 sheet: 0.78 (0.35), residues: 200 loop : 0.19 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.023 0.002 TYR A 170 PHE 0.013 0.002 PHE H 50 TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 4003) covalent geometry : angle 0.53731 ( 5459) SS BOND : bond 0.00302 ( 5) SS BOND : angle 0.56778 ( 10) hydrogen bonds : bond 0.03008 ( 155) hydrogen bonds : angle 5.67723 ( 402) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 1.63712 ( 9) link_NAG-ASN : bond 0.00334 ( 6) link_NAG-ASN : angle 2.75432 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 0.0935 time to fit residues: 4.9480 Evaluate side-chains 41 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 23 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.104630 restraints weight = 4259.739| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.24 r_work: 0.2879 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4017 Z= 0.140 Angle : 0.532 8.720 5496 Z= 0.268 Chirality : 0.046 0.330 624 Planarity : 0.003 0.030 691 Dihedral : 4.387 17.695 723 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.97 % Allowed : 6.18 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.38), residues: 482 helix: -0.23 (1.42), residues: 17 sheet: 0.67 (0.35), residues: 203 loop : 0.28 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.020 0.001 TYR A 170 PHE 0.012 0.001 PHE A 133 TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4003) covalent geometry : angle 0.50989 ( 5459) SS BOND : bond 0.00221 ( 5) SS BOND : angle 0.43080 ( 10) hydrogen bonds : bond 0.02766 ( 155) hydrogen bonds : angle 5.52341 ( 402) link_BETA1-4 : bond 0.00391 ( 3) link_BETA1-4 : angle 1.53993 ( 9) link_NAG-ASN : bond 0.00307 ( 6) link_NAG-ASN : angle 2.50715 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.158 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.0903 time to fit residues: 4.8014 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106198 restraints weight = 4201.863| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.23 r_work: 0.2898 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4017 Z= 0.154 Angle : 0.533 8.304 5496 Z= 0.269 Chirality : 0.046 0.304 624 Planarity : 0.004 0.030 691 Dihedral : 4.257 16.782 723 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.69 % Allowed : 6.18 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.38), residues: 482 helix: 2.67 (1.60), residues: 11 sheet: 0.56 (0.35), residues: 204 loop : 0.29 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.019 0.001 TYR A 170 PHE 0.012 0.001 PHE A 133 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4003) covalent geometry : angle 0.51241 ( 5459) SS BOND : bond 0.00229 ( 5) SS BOND : angle 0.49325 ( 10) hydrogen bonds : bond 0.02772 ( 155) hydrogen bonds : angle 5.49090 ( 402) link_BETA1-4 : bond 0.00383 ( 3) link_BETA1-4 : angle 1.53444 ( 9) link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 2.44120 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.183 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0909 time to fit residues: 4.5849 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115120 restraints weight = 4146.436| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.18 r_work: 0.2732 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4017 Z= 0.162 Angle : 0.538 8.076 5496 Z= 0.271 Chirality : 0.046 0.287 624 Planarity : 0.004 0.030 691 Dihedral : 4.250 16.587 723 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.25 % Allowed : 5.34 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.38), residues: 482 helix: 2.69 (1.60), residues: 11 sheet: 0.52 (0.35), residues: 204 loop : 0.32 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.021 0.002 TYR A 170 PHE 0.013 0.001 PHE A 133 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4003) covalent geometry : angle 0.51771 ( 5459) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.50932 ( 10) hydrogen bonds : bond 0.02778 ( 155) hydrogen bonds : angle 5.47939 ( 402) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 1.52258 ( 9) link_NAG-ASN : bond 0.00309 ( 6) link_NAG-ASN : angle 2.37940 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8523 (mtm180) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.0951 time to fit residues: 4.9995 Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 15 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115134 restraints weight = 4141.107| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.19 r_work: 0.2731 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4017 Z= 0.163 Angle : 0.543 7.980 5496 Z= 0.272 Chirality : 0.046 0.284 624 Planarity : 0.004 0.030 691 Dihedral : 4.259 16.394 723 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.97 % Allowed : 5.90 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.38), residues: 482 helix: 2.68 (1.60), residues: 11 sheet: 0.56 (0.35), residues: 203 loop : 0.33 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.021 0.002 TYR A 170 PHE 0.013 0.001 PHE A 133 TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4003) covalent geometry : angle 0.52324 ( 5459) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.53047 ( 10) hydrogen bonds : bond 0.02781 ( 155) hydrogen bonds : angle 5.47938 ( 402) link_BETA1-4 : bond 0.00372 ( 3) link_BETA1-4 : angle 1.52580 ( 9) link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 2.34929 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 964 Ramachandran restraints generated. 482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8508 (mtm180) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.0856 time to fit residues: 4.2985 Evaluate side-chains 42 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 237 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.146361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114626 restraints weight = 4153.336| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.18 r_work: 0.2720 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4017 Z= 0.173 Angle : 0.549 7.964 5496 Z= 0.275 Chirality : 0.046 0.277 624 Planarity : 0.004 0.030 691 Dihedral : 4.297 16.279 723 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.25 % Allowed : 5.62 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.38), residues: 482 helix: 2.73 (1.61), residues: 11 sheet: 0.65 (0.35), residues: 200 loop : 0.26 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.021 0.002 TYR A 170 PHE 0.013 0.002 PHE A 133 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 4003) covalent geometry : angle 0.53017 ( 5459) SS BOND : bond 0.00258 ( 5) SS BOND : angle 0.52759 ( 10) hydrogen bonds : bond 0.02819 ( 155) hydrogen bonds : angle 5.50588 ( 402) link_BETA1-4 : bond 0.00350 ( 3) link_BETA1-4 : angle 1.53977 ( 9) link_NAG-ASN : bond 0.00308 ( 6) link_NAG-ASN : angle 2.34260 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1381.14 seconds wall clock time: 24 minutes 26.63 seconds (1466.63 seconds total)