Starting phenix.real_space_refine on Fri Aug 22 22:48:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fe1_50336/08_2025/9fe1_50336.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fe1_50336/08_2025/9fe1_50336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fe1_50336/08_2025/9fe1_50336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fe1_50336/08_2025/9fe1_50336.map" model { file = "/net/cci-nas-00/data/ceres_data/9fe1_50336/08_2025/9fe1_50336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fe1_50336/08_2025/9fe1_50336.cif" } resolution = 3.1 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= 1.000 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: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 2706 2.51 5 N 767 2.21 5 O 809 1.98 5 H 4163 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8458 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4325 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 262} Chain: "B" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1622 Classifications: {'peptide': 99} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 159 Classifications: {'peptide': 9} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 8} Chain: "D" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 2352 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 4, 'TRANS': 152} Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8458 At special positions: 0 Unit cell: (63.375, 68.25, 103.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 809 8.00 N 767 7.00 C 2706 6.00 H 4163 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.04 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 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 339.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 6 sheets defined 34.5% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 56 through 85 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.553A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 92 through 103 Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 125 through 135 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 158 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.706A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS A 114 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR A 118 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.173A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 218 removed outlier: 3.633A pdb=" N THR A 216 " --> pdb=" O HIS A 260 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 260 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN A 218 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR A 258 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.504A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.504A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 228 hydrogen bonds defined for protein. 633 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: 1.95 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4163 1.03 - 1.23: 2 1.23 - 1.42: 1901 1.42 - 1.62: 2475 1.62 - 1.82: 20 Bond restraints: 8561 Sorted by residual: bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 bond pdb=" N ASP D 13 " pdb=" CA ASP D 13 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" CG1 ILE D 95 " pdb=" CD1 ILE D 95 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.81e+00 bond pdb=" CD2 TYR A 113 " pdb=" CE2 TYR A 113 " ideal model delta sigma weight residual 1.382 1.335 0.047 3.00e-02 1.11e+03 2.46e+00 bond pdb=" N ASP D 13 " pdb=" H ASP D 13 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 8556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14900 1.70 - 3.39: 481 3.39 - 5.09: 39 5.09 - 6.78: 3 6.78 - 8.48: 4 Bond angle restraints: 15427 Sorted by residual: angle pdb=" N GLY A 56 " pdb=" CA GLY A 56 " pdb=" C GLY A 56 " ideal model delta sigma weight residual 112.34 120.36 -8.02 2.04e+00 2.40e-01 1.55e+01 angle pdb=" CA ARG A 170 " pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " ideal model delta sigma weight residual 114.10 106.64 7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB LYS D 17 " pdb=" CG LYS D 17 " pdb=" CD LYS D 17 " ideal model delta sigma weight residual 111.30 119.78 -8.48 2.30e+00 1.89e-01 1.36e+01 angle pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " pdb=" CD ARG A 170 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 angle pdb=" N LEU B 54 " pdb=" CA LEU B 54 " pdb=" C LEU B 54 " ideal model delta sigma weight residual 109.96 114.85 -4.89 1.49e+00 4.50e-01 1.08e+01 ... (remaining 15422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 3623 17.40 - 34.80: 268 34.80 - 52.20: 73 52.20 - 69.60: 46 69.60 - 87.00: 15 Dihedral angle restraints: 4025 sinusoidal: 2151 harmonic: 1874 Sorted by residual: dihedral pdb=" CA PRO B 5 " pdb=" C PRO B 5 " pdb=" N LYS B 6 " pdb=" CA LYS B 6 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ILE B 35 " pdb=" C ILE B 35 " pdb=" N GLU B 36 " pdb=" CA GLU B 36 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ARG A 181 " pdb=" C ARG A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 4022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 414 0.043 - 0.085: 166 0.085 - 0.127: 45 0.127 - 0.169: 11 0.169 - 0.212: 5 Chirality restraints: 641 Sorted by residual: chirality pdb=" CA ARG A 170 " pdb=" N ARG A 170 " pdb=" C ARG A 170 " pdb=" CB ARG A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A 57 " pdb=" N PRO A 57 " pdb=" C PRO A 57 " pdb=" CB PRO A 57 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LYS A 68 " pdb=" N LYS A 68 " pdb=" C LYS A 68 " pdb=" CB LYS A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 638 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 52 " 0.011 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" CG HIS D 52 " 0.005 2.00e-02 2.50e+03 pdb=" ND1 HIS D 52 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS D 52 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 HIS D 52 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS D 52 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS D 52 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 HIS D 52 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 HIS D 52 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " 0.374 9.50e-02 1.11e+02 1.26e-01 2.19e+01 pdb=" NE ARG A 48 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.006 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 56 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO A 57 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.057 5.00e-02 4.00e+02 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 396 2.15 - 2.76: 16140 2.76 - 3.37: 24385 3.37 - 3.99: 31696 3.99 - 4.60: 49229 Nonbonded interactions: 121846 Sorted by model distance: nonbonded pdb=" HH TYR A 159 " pdb=" O SER C 1 " model vdw 1.537 2.450 nonbonded pdb=" HG SER B 11 " pdb=" O HIS B 13 " model vdw 1.546 2.450 nonbonded pdb=" O ASP A 129 " pdb="HH11 ARG A 131 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLU D 127 " pdb=" H GLU D 127 " model vdw 1.557 2.450 nonbonded pdb=" O TRP A 60 " pdb=" HG1 THR A 64 " model vdw 1.560 2.450 ... (remaining 121841 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: 1.440 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: 0.060 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.420 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 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 : 0.005 0.065 4401 Z= 0.207 Angle : 0.835 8.481 5969 Z= 0.483 Chirality : 0.051 0.212 641 Planarity : 0.012 0.165 775 Dihedral : 15.082 87.003 1598 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.22 % Allowed : 2.23 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.63 (0.32), residues: 531 helix: -1.80 (0.32), residues: 187 sheet: 0.85 (0.45), residues: 110 loop : -1.31 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.005 ARG A 48 TYR 0.029 0.007 TYR A 171 PHE 0.020 0.003 PHE B 30 TRP 0.040 0.005 TRP A 60 HIS 0.010 0.002 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 4398) covalent geometry : angle 0.83420 ( 5963) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.24223 ( 6) hydrogen bonds : bond 0.19822 ( 213) hydrogen bonds : angle 7.75791 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 102 average time/residue: 0.2881 time to fit residues: 33.6517 Evaluate side-chains 52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.124477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.105463 restraints weight = 23099.739| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.68 r_work: 0.3746 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4401 Z= 0.166 Angle : 0.629 5.286 5969 Z= 0.342 Chirality : 0.041 0.149 641 Planarity : 0.005 0.060 775 Dihedral : 6.214 59.570 591 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.00 % Allowed : 8.46 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.31 (0.34), residues: 531 helix: 0.60 (0.35), residues: 181 sheet: 0.69 (0.43), residues: 113 loop : -0.23 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 170 TYR 0.015 0.002 TYR A 171 PHE 0.015 0.002 PHE D 123 TRP 0.014 0.002 TRP A 60 HIS 0.007 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4398) covalent geometry : angle 0.62892 ( 5963) SS BOND : bond 0.00401 ( 3) SS BOND : angle 1.00491 ( 6) hydrogen bonds : bond 0.04743 ( 213) hydrogen bonds : angle 5.49782 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 58 average time/residue: 0.1827 time to fit residues: 13.0695 Evaluate side-chains 52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain C residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.124744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105402 restraints weight = 23120.916| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.72 r_work: 0.3756 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4401 Z= 0.128 Angle : 0.564 5.594 5969 Z= 0.304 Chirality : 0.039 0.154 641 Planarity : 0.004 0.044 775 Dihedral : 5.739 58.842 591 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 9.13 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.92 (0.35), residues: 531 helix: 1.55 (0.37), residues: 181 sheet: 0.53 (0.40), residues: 123 loop : -0.01 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 81 TYR 0.009 0.002 TYR B 67 PHE 0.010 0.001 PHE A 9 TRP 0.016 0.001 TRP A 204 HIS 0.007 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4398) covalent geometry : angle 0.56205 ( 5963) SS BOND : bond 0.00668 ( 3) SS BOND : angle 1.66509 ( 6) hydrogen bonds : bond 0.04073 ( 213) hydrogen bonds : angle 4.93847 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.1691 time to fit residues: 12.1475 Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.122671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103429 restraints weight = 23588.713| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.73 r_work: 0.3709 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4401 Z= 0.142 Angle : 0.551 5.269 5969 Z= 0.295 Chirality : 0.039 0.147 641 Planarity : 0.003 0.039 775 Dihedral : 5.701 59.274 591 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.00 % Allowed : 10.24 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.87 (0.34), residues: 531 helix: 1.58 (0.36), residues: 181 sheet: 0.45 (0.40), residues: 123 loop : -0.08 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.011 0.002 TYR A 116 PHE 0.010 0.001 PHE A 9 TRP 0.013 0.001 TRP A 51 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4398) covalent geometry : angle 0.55023 ( 5963) SS BOND : bond 0.00941 ( 3) SS BOND : angle 1.17327 ( 6) hydrogen bonds : bond 0.03871 ( 213) hydrogen bonds : angle 4.74045 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7686 (tp30) cc_final: 0.7385 (tp30) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1608 time to fit residues: 11.1522 Evaluate side-chains 52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.120699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.101477 restraints weight = 23782.605| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.74 r_work: 0.3672 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4401 Z= 0.178 Angle : 0.573 5.083 5969 Z= 0.308 Chirality : 0.040 0.145 641 Planarity : 0.004 0.038 775 Dihedral : 5.729 53.348 591 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 10.02 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.48 (0.34), residues: 531 helix: 1.14 (0.36), residues: 181 sheet: -0.03 (0.40), residues: 133 loop : 0.01 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 6 TYR 0.010 0.002 TYR A 113 PHE 0.012 0.002 PHE A 9 TRP 0.015 0.002 TRP A 51 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4398) covalent geometry : angle 0.57173 ( 5963) SS BOND : bond 0.00831 ( 3) SS BOND : angle 1.36884 ( 6) hydrogen bonds : bond 0.03931 ( 213) hydrogen bonds : angle 4.79022 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7658 (tp30) cc_final: 0.7422 (tp30) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.1670 time to fit residues: 10.7848 Evaluate side-chains 50 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.121277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102370 restraints weight = 23404.653| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.69 r_work: 0.3696 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.140 Angle : 0.537 5.287 5969 Z= 0.287 Chirality : 0.039 0.142 641 Planarity : 0.003 0.035 775 Dihedral : 5.525 50.912 591 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.90 % Allowed : 10.47 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.35), residues: 531 helix: 1.29 (0.36), residues: 181 sheet: -0.33 (0.40), residues: 146 loop : 0.29 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.010 0.002 TYR A 99 PHE 0.009 0.001 PHE A 9 TRP 0.011 0.001 TRP A 60 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4398) covalent geometry : angle 0.53633 ( 5963) SS BOND : bond 0.00677 ( 3) SS BOND : angle 1.06242 ( 6) hydrogen bonds : bond 0.03667 ( 213) hydrogen bonds : angle 4.61272 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7639 (tp30) cc_final: 0.7395 (tp30) REVERT: B 96 ASP cc_start: 0.7460 (t70) cc_final: 0.7038 (t0) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.1637 time to fit residues: 11.3503 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.102775 restraints weight = 23710.831| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.78 r_work: 0.3700 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.122 Angle : 0.526 5.233 5969 Z= 0.282 Chirality : 0.038 0.141 641 Planarity : 0.003 0.034 775 Dihedral : 5.358 47.827 591 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.67 % Allowed : 11.58 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.73 (0.36), residues: 531 helix: 1.49 (0.37), residues: 181 sheet: -0.32 (0.40), residues: 146 loop : 0.41 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.010 0.001 TYR A 99 PHE 0.008 0.001 PHE A 9 TRP 0.010 0.001 TRP A 60 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4398) covalent geometry : angle 0.52485 ( 5963) SS BOND : bond 0.00639 ( 3) SS BOND : angle 1.01497 ( 6) hydrogen bonds : bond 0.03508 ( 213) hydrogen bonds : angle 4.47320 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7607 (tp30) cc_final: 0.7395 (tp30) REVERT: B 96 ASP cc_start: 0.7619 (t0) cc_final: 0.6980 (t0) REVERT: B 98 ASP cc_start: 0.4983 (p0) cc_final: 0.4487 (p0) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.1260 time to fit residues: 9.3900 Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.122152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103325 restraints weight = 23331.310| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.70 r_work: 0.3714 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.113 Angle : 0.513 5.278 5969 Z= 0.274 Chirality : 0.038 0.139 641 Planarity : 0.003 0.033 775 Dihedral : 5.188 44.128 591 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.45 % Allowed : 12.03 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.80 (0.36), residues: 531 helix: 1.64 (0.37), residues: 181 sheet: -0.55 (0.40), residues: 152 loop : 0.63 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 273 TYR 0.011 0.001 TYR A 99 PHE 0.007 0.001 PHE A 9 TRP 0.009 0.001 TRP A 60 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4398) covalent geometry : angle 0.51291 ( 5963) SS BOND : bond 0.00604 ( 3) SS BOND : angle 0.91293 ( 6) hydrogen bonds : bond 0.03385 ( 213) hydrogen bonds : angle 4.39552 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7618 (tp30) cc_final: 0.7407 (tp30) REVERT: B 96 ASP cc_start: 0.7661 (t0) cc_final: 0.7061 (t0) REVERT: B 98 ASP cc_start: 0.4997 (p0) cc_final: 0.4534 (p0) outliers start: 11 outliers final: 11 residues processed: 55 average time/residue: 0.1380 time to fit residues: 9.5124 Evaluate side-chains 56 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.122503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.103472 restraints weight = 23696.544| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.71 r_work: 0.3715 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.120 Angle : 0.514 5.235 5969 Z= 0.277 Chirality : 0.038 0.138 641 Planarity : 0.003 0.033 775 Dihedral : 5.165 44.489 591 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.23 % Allowed : 12.92 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.78 (0.36), residues: 531 helix: 1.67 (0.37), residues: 181 sheet: -0.55 (0.40), residues: 152 loop : 0.55 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 97 TYR 0.010 0.001 TYR A 99 PHE 0.007 0.001 PHE A 9 TRP 0.008 0.001 TRP A 60 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4398) covalent geometry : angle 0.51352 ( 5963) SS BOND : bond 0.00574 ( 3) SS BOND : angle 0.82873 ( 6) hydrogen bonds : bond 0.03394 ( 213) hydrogen bonds : angle 4.38118 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ASP cc_start: 0.7661 (t0) cc_final: 0.7363 (m-30) REVERT: B 98 ASP cc_start: 0.5199 (p0) cc_final: 0.4934 (p0) outliers start: 10 outliers final: 10 residues processed: 53 average time/residue: 0.1398 time to fit residues: 9.4408 Evaluate side-chains 54 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.122069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102957 restraints weight = 23819.954| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.71 r_work: 0.3706 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4401 Z= 0.132 Angle : 0.527 5.244 5969 Z= 0.283 Chirality : 0.038 0.138 641 Planarity : 0.003 0.033 775 Dihedral : 5.204 46.912 591 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.45 % Allowed : 12.92 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.36), residues: 531 helix: 1.59 (0.37), residues: 181 sheet: -0.65 (0.40), residues: 152 loop : 0.45 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.011 0.002 TYR A 99 PHE 0.008 0.001 PHE D 123 TRP 0.008 0.001 TRP A 60 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4398) covalent geometry : angle 0.52612 ( 5963) SS BOND : bond 0.00568 ( 3) SS BOND : angle 0.83888 ( 6) hydrogen bonds : bond 0.03439 ( 213) hydrogen bonds : angle 4.42509 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ASP cc_start: 0.7691 (t0) cc_final: 0.7339 (m-30) REVERT: B 98 ASP cc_start: 0.5164 (p0) cc_final: 0.4917 (p0) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.1560 time to fit residues: 10.4980 Evaluate side-chains 53 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.102541 restraints weight = 23598.291| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.72 r_work: 0.3698 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4401 Z= 0.139 Angle : 0.534 5.216 5969 Z= 0.286 Chirality : 0.038 0.136 641 Planarity : 0.003 0.033 775 Dihedral : 5.212 47.113 591 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.45 % Allowed : 13.14 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.57 (0.36), residues: 531 helix: 1.52 (0.37), residues: 181 sheet: -0.67 (0.40), residues: 152 loop : 0.40 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.011 0.002 TYR A 99 PHE 0.008 0.001 PHE D 123 TRP 0.009 0.001 TRP A 60 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4398) covalent geometry : angle 0.53320 ( 5963) SS BOND : bond 0.00571 ( 3) SS BOND : angle 0.92942 ( 6) hydrogen bonds : bond 0.03478 ( 213) hydrogen bonds : angle 4.44898 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.65 seconds wall clock time: 46 minutes 22.90 seconds (2782.90 seconds total)