Starting phenix.real_space_refine on Tue Feb 3 21:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s36_54524/02_2026/9s36_54524_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s36_54524/02_2026/9s36_54524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s36_54524/02_2026/9s36_54524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s36_54524/02_2026/9s36_54524.map" model { file = "/net/cci-nas-00/data/ceres_data/9s36_54524/02_2026/9s36_54524_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s36_54524/02_2026/9s36_54524_trim.cif" } resolution = 3.4 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= 0.021 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 18 5.16 5 C 2246 2.51 5 N 552 2.21 5 O 637 1.98 5 H 3451 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6906 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 4964 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 6, 'TRANS': 308} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1903 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.19, per 1000 atoms: 0.17 Number of scatterers: 6906 At special positions: 0 Unit cell: (88.572, 75.396, 66.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 2 15.00 O 637 8.00 N 552 7.00 C 2246 6.00 H 3451 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 203.7 milliseconds 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 65.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.641A pdb=" N GLY A 80 " --> pdb=" O TYR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 108 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 123 through 144 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 154 through 167 removed outlier: 4.024A pdb=" N ILE A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 166 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 196 Processing helix chain 'A' and resid 204 through 236 removed outlier: 4.013A pdb=" N LYS A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 262 removed outlier: 4.006A pdb=" N ILE A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 277 through 318 removed outlier: 3.727A pdb=" N VAL A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 removed outlier: 3.624A pdb=" N GLY A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 362 removed outlier: 3.580A pdb=" N PHE A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.954A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.747A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.511A pdb=" N ALA B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG B 37 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE B 46 " --> pdb=" O ARG B 37 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 693 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: 1.40 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3445 1.03 - 1.23: 8 1.23 - 1.42: 1518 1.42 - 1.61: 1986 1.61 - 1.81: 32 Bond restraints: 6989 Sorted by residual: bond pdb=" N LEU A 48 " pdb=" CA LEU A 48 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N LEU A 48 " pdb=" H LEU A 48 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C GLY A 80 " pdb=" N PHE A 81 " ideal model delta sigma weight residual 1.332 1.317 0.016 1.40e-02 5.10e+03 1.26e+00 bond pdb=" CB GLN B 12 " pdb=" CG GLN B 12 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.72e-01 bond pdb=" C ILE B 109 " pdb=" N PRO B 110 " ideal model delta sigma weight residual 1.337 1.347 -0.010 1.24e-02 6.50e+03 6.56e-01 ... (remaining 6984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 11788 1.03 - 2.06: 758 2.06 - 3.09: 22 3.09 - 4.12: 11 4.12 - 5.15: 4 Bond angle restraints: 12583 Sorted by residual: angle pdb=" CA GLU B 108 " pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " ideal model delta sigma weight residual 114.10 118.54 -4.44 2.00e+00 2.50e-01 4.93e+00 angle pdb=" CA TRP B 111 " pdb=" CB TRP B 111 " pdb=" CG TRP B 111 " ideal model delta sigma weight residual 113.60 117.69 -4.09 1.90e+00 2.77e-01 4.63e+00 angle pdb=" CB GLN B 12 " pdb=" CG GLN B 12 " pdb=" CD GLN B 12 " ideal model delta sigma weight residual 112.60 115.95 -3.35 1.70e+00 3.46e-01 3.89e+00 angle pdb=" C ASP A 202 " pdb=" N ASP A 203 " pdb=" CA ASP A 203 " ideal model delta sigma weight residual 121.54 124.97 -3.43 1.91e+00 2.74e-01 3.23e+00 angle pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " pdb=" CD GLU B 108 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.70e+00 3.46e-01 3.22e+00 ... (remaining 12578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 3087 21.69 - 43.39: 205 43.39 - 65.08: 53 65.08 - 86.77: 4 86.77 - 108.47: 1 Dihedral angle restraints: 3350 sinusoidal: 1772 harmonic: 1578 Sorted by residual: dihedral pdb=" C41 GDD A 401 " pdb=" C51 GDD A 401 " pdb=" C61 GDD A 401 " pdb=" O6A GDD A 401 " ideal model delta sinusoidal sigma weight residual 186.12 77.65 108.47 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" CA GLY A 80 " pdb=" C GLY A 80 " pdb=" N PHE A 81 " pdb=" CA PHE A 81 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " pdb=" CG LEU A 249 " pdb=" CD1 LEU A 249 " ideal model delta sinusoidal sigma weight residual 180.00 120.20 59.80 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 392 0.029 - 0.057: 103 0.057 - 0.086: 45 0.086 - 0.114: 19 0.114 - 0.143: 4 Chirality restraints: 563 Sorted by residual: chirality pdb=" CA TRP B 111 " pdb=" N TRP B 111 " pdb=" C TRP B 111 " pdb=" CB TRP B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE B 109 " pdb=" N ILE B 109 " pdb=" C ILE B 109 " pdb=" CB ILE B 109 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE A 110 " pdb=" N ILE A 110 " pdb=" C ILE A 110 " pdb=" CB ILE A 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 560 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 113 " 0.182 9.50e-02 1.11e+02 6.08e-02 4.28e+00 pdb=" NE ARG A 113 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 113 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 113 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 113 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 113 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 113 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 113 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 321 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 109 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 110 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " -0.021 5.00e-02 4.00e+02 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.41: 3026 2.41 - 2.96: 15436 2.96 - 3.51: 17708 3.51 - 4.05: 23229 4.05 - 4.60: 34310 Nonbonded interactions: 93709 Sorted by model distance: nonbonded pdb=" HB3 LYS B 86 " pdb=" HZ2 LYS B 86 " model vdw 1.869 2.270 nonbonded pdb=" H ASN A 84 " pdb=" H LEU A 85 " model vdw 1.898 2.100 nonbonded pdb=" H THR A 235 " pdb=" HG1 THR A 235 " model vdw 1.905 2.100 nonbonded pdb=" H ILE A 134 " pdb="HG12 ILE A 134 " model vdw 1.913 2.270 nonbonded pdb=" HG2 ARG A 113 " pdb="HH11 ARG A 113 " model vdw 1.914 2.270 ... (remaining 93704 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: 3.630 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: 0.030 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.890 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 : 0.002 0.033 3539 Z= 0.110 Angle : 0.458 5.147 4819 Z= 0.264 Chirality : 0.036 0.143 563 Planarity : 0.005 0.080 581 Dihedral : 15.556 108.469 1260 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.54 % Allowed : 18.60 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.67 (0.39), residues: 437 helix: -0.18 (0.30), residues: 267 sheet: -0.28 (0.77), residues: 57 loop : -0.76 (0.57), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 113 TYR 0.005 0.001 TYR B 31 PHE 0.005 0.001 PHE A 240 TRP 0.011 0.001 TRP B 111 HIS 0.000 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3538) covalent geometry : angle 0.45799 ( 4817) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.09120 ( 2) hydrogen bonds : bond 0.21933 ( 235) hydrogen bonds : angle 8.53486 ( 693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.7477 (t80) cc_final: 0.7249 (t80) outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.1436 time to fit residues: 11.0368 Evaluate side-chains 47 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087784 restraints weight = 20519.096| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.51 r_work: 0.3085 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3539 Z= 0.187 Angle : 0.519 4.858 4819 Z= 0.297 Chirality : 0.037 0.148 563 Planarity : 0.005 0.048 581 Dihedral : 8.392 103.675 530 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.70 % Allowed : 18.06 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.53 (0.41), residues: 437 helix: 2.04 (0.31), residues: 263 sheet: -0.05 (0.75), residues: 57 loop : -0.77 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 113 TYR 0.007 0.001 TYR A 76 PHE 0.006 0.001 PHE A 240 TRP 0.013 0.001 TRP B 111 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 3538) covalent geometry : angle 0.51931 ( 4817) SS BOND : bond 0.00344 ( 1) SS BOND : angle 0.79190 ( 2) hydrogen bonds : bond 0.05734 ( 235) hydrogen bonds : angle 4.77252 ( 693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 20 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8878 (p) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.1486 time to fit residues: 10.1617 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088465 restraints weight = 20488.712| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.52 r_work: 0.3090 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3539 Z= 0.149 Angle : 0.468 4.797 4819 Z= 0.262 Chirality : 0.036 0.144 563 Planarity : 0.004 0.047 581 Dihedral : 7.870 95.895 528 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.43 % Allowed : 17.25 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.12 (0.41), residues: 437 helix: 2.65 (0.31), residues: 261 sheet: 0.07 (0.71), residues: 57 loop : -0.78 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 229 TYR 0.006 0.001 TYR A 311 PHE 0.005 0.001 PHE B 94 TRP 0.012 0.001 TRP B 111 HIS 0.001 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3538) covalent geometry : angle 0.46853 ( 4817) SS BOND : bond 0.00335 ( 1) SS BOND : angle 0.33162 ( 2) hydrogen bonds : bond 0.04734 ( 235) hydrogen bonds : angle 4.30622 ( 693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8052 (t80) cc_final: 0.7756 (t80) REVERT: B 31 TYR cc_start: 0.8700 (m-80) cc_final: 0.8439 (m-80) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1926 time to fit residues: 12.6106 Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.099513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088634 restraints weight = 20741.180| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.54 r_work: 0.3087 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3539 Z= 0.124 Angle : 0.452 4.752 4819 Z= 0.250 Chirality : 0.036 0.140 563 Planarity : 0.004 0.051 581 Dihedral : 7.456 85.424 528 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.43 % Allowed : 15.90 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.36 (0.41), residues: 437 helix: 2.85 (0.31), residues: 262 sheet: 0.12 (0.70), residues: 57 loop : -0.75 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.005 0.001 PHE A 83 TRP 0.011 0.001 TRP B 111 HIS 0.000 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3538) covalent geometry : angle 0.45176 ( 4817) SS BOND : bond 0.00319 ( 1) SS BOND : angle 0.24012 ( 2) hydrogen bonds : bond 0.04089 ( 235) hydrogen bonds : angle 4.04119 ( 693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9089 (tpp) cc_final: 0.8234 (tpp) REVERT: A 336 PHE cc_start: 0.8017 (t80) cc_final: 0.7734 (t80) REVERT: B 31 TYR cc_start: 0.8659 (m-80) cc_final: 0.8388 (m-80) outliers start: 9 outliers final: 5 residues processed: 55 average time/residue: 0.1917 time to fit residues: 12.5809 Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 4 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088479 restraints weight = 20822.308| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.52 r_work: 0.3069 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3539 Z= 0.134 Angle : 0.449 4.739 4819 Z= 0.250 Chirality : 0.036 0.142 563 Planarity : 0.004 0.054 581 Dihedral : 7.137 75.409 528 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 17.25 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.45 (0.41), residues: 437 helix: 2.92 (0.31), residues: 262 sheet: 0.26 (0.68), residues: 57 loop : -0.76 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.005 0.001 PHE B 94 TRP 0.012 0.001 TRP B 111 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3538) covalent geometry : angle 0.44862 ( 4817) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.17074 ( 2) hydrogen bonds : bond 0.03895 ( 235) hydrogen bonds : angle 3.91028 ( 693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 PHE cc_start: 0.7997 (t80) cc_final: 0.7730 (t80) REVERT: B 31 TYR cc_start: 0.8661 (m-80) cc_final: 0.8439 (m-80) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 0.1757 time to fit residues: 11.1470 Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.099001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088563 restraints weight = 20669.499| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.53 r_work: 0.3082 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3539 Z= 0.146 Angle : 0.452 4.757 4819 Z= 0.252 Chirality : 0.036 0.141 563 Planarity : 0.004 0.055 581 Dihedral : 6.883 72.268 528 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.50 % Allowed : 16.71 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.52 (0.41), residues: 437 helix: 2.98 (0.31), residues: 263 sheet: 0.43 (0.68), residues: 57 loop : -0.89 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.005 0.001 PHE B 94 TRP 0.012 0.001 TRP B 111 HIS 0.000 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3538) covalent geometry : angle 0.45236 ( 4817) SS BOND : bond 0.00237 ( 1) SS BOND : angle 0.16095 ( 2) hydrogen bonds : bond 0.03810 ( 235) hydrogen bonds : angle 3.82269 ( 693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8728 (m) REVERT: A 336 PHE cc_start: 0.7974 (t80) cc_final: 0.7725 (t80) REVERT: B 5 GLU cc_start: 0.8731 (mp0) cc_final: 0.8308 (mp0) outliers start: 13 outliers final: 8 residues processed: 59 average time/residue: 0.1611 time to fit residues: 11.4240 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.099220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088881 restraints weight = 20382.057| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.47 r_work: 0.3102 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3539 Z= 0.133 Angle : 0.448 4.763 4819 Z= 0.248 Chirality : 0.036 0.138 563 Planarity : 0.004 0.044 581 Dihedral : 6.348 67.794 528 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.50 % Allowed : 17.25 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.60 (0.41), residues: 437 helix: 3.04 (0.31), residues: 263 sheet: 0.52 (0.69), residues: 57 loop : -0.87 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.006 0.001 PHE A 219 TRP 0.012 0.001 TRP B 111 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3538) covalent geometry : angle 0.44811 ( 4817) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.14615 ( 2) hydrogen bonds : bond 0.03701 ( 235) hydrogen bonds : angle 3.71975 ( 693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8718 (m) REVERT: A 336 PHE cc_start: 0.7956 (t80) cc_final: 0.7722 (t80) REVERT: A 360 GLN cc_start: 0.8248 (mp10) cc_final: 0.7900 (mp10) REVERT: B 5 GLU cc_start: 0.8711 (mp0) cc_final: 0.8291 (mp0) REVERT: B 31 TYR cc_start: 0.8653 (m-80) cc_final: 0.8389 (m-80) outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 0.1541 time to fit residues: 11.0616 Evaluate side-chains 57 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.099848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089572 restraints weight = 20575.035| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.48 r_work: 0.3105 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3539 Z= 0.124 Angle : 0.448 4.848 4819 Z= 0.247 Chirality : 0.036 0.136 563 Planarity : 0.004 0.060 581 Dihedral : 5.671 63.335 528 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.70 % Allowed : 18.06 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.69 (0.41), residues: 437 helix: 3.10 (0.31), residues: 262 sheet: 0.60 (0.69), residues: 57 loop : -0.77 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.006 0.001 PHE B 94 TRP 0.011 0.001 TRP B 111 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3538) covalent geometry : angle 0.44782 ( 4817) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.12120 ( 2) hydrogen bonds : bond 0.03580 ( 235) hydrogen bonds : angle 3.62908 ( 693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8703 (m) REVERT: A 336 PHE cc_start: 0.7942 (t80) cc_final: 0.7713 (t80) REVERT: A 360 GLN cc_start: 0.8265 (mp10) cc_final: 0.7879 (mp10) REVERT: B 5 GLU cc_start: 0.8697 (mp0) cc_final: 0.8280 (mp0) REVERT: B 31 TYR cc_start: 0.8637 (m-80) cc_final: 0.8382 (m-80) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1362 time to fit residues: 9.3508 Evaluate side-chains 56 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.100991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090623 restraints weight = 20474.703| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.49 r_work: 0.3121 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3539 Z= 0.111 Angle : 0.447 5.635 4819 Z= 0.246 Chirality : 0.036 0.133 563 Planarity : 0.004 0.048 581 Dihedral : 5.151 57.451 528 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.62 % Allowed : 19.41 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.79 (0.41), residues: 437 helix: 3.20 (0.31), residues: 264 sheet: 0.40 (0.71), residues: 51 loop : -0.66 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.007 0.001 TYR A 311 PHE 0.005 0.001 PHE B 94 TRP 0.011 0.001 TRP B 111 HIS 0.000 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3538) covalent geometry : angle 0.44706 ( 4817) SS BOND : bond 0.00248 ( 1) SS BOND : angle 0.12447 ( 2) hydrogen bonds : bond 0.03445 ( 235) hydrogen bonds : angle 3.52247 ( 693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8680 (m) REVERT: A 336 PHE cc_start: 0.7906 (t80) cc_final: 0.7695 (t80) REVERT: A 360 GLN cc_start: 0.8264 (mp10) cc_final: 0.7868 (mp10) REVERT: B 5 GLU cc_start: 0.8683 (mp0) cc_final: 0.8278 (mp0) REVERT: B 31 TYR cc_start: 0.8602 (m-80) cc_final: 0.8327 (m-80) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.1911 time to fit residues: 12.0720 Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.099862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089451 restraints weight = 20650.342| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.49 r_work: 0.3112 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3539 Z= 0.143 Angle : 0.465 5.290 4819 Z= 0.257 Chirality : 0.036 0.138 563 Planarity : 0.004 0.048 581 Dihedral : 5.190 57.101 528 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.08 % Allowed : 20.49 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.78 (0.41), residues: 437 helix: 3.19 (0.31), residues: 262 sheet: 0.58 (0.68), residues: 57 loop : -0.78 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.007 0.001 PHE A 219 TRP 0.011 0.001 TRP B 111 HIS 0.000 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3538) covalent geometry : angle 0.46533 ( 4817) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.24149 ( 2) hydrogen bonds : bond 0.03584 ( 235) hydrogen bonds : angle 3.57310 ( 693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 874 Ramachandran restraints generated. 437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8724 (m) REVERT: A 336 PHE cc_start: 0.7959 (t80) cc_final: 0.7738 (t80) REVERT: B 5 GLU cc_start: 0.8727 (mp0) cc_final: 0.8313 (mp0) REVERT: B 31 TYR cc_start: 0.8650 (m-80) cc_final: 0.8389 (m-80) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.1553 time to fit residues: 9.5502 Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain B residue 75 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.100608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.090304 restraints weight = 20439.237| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.47 r_work: 0.3125 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3539 Z= 0.127 Angle : 0.465 5.893 4819 Z= 0.257 Chirality : 0.036 0.136 563 Planarity : 0.004 0.047 581 Dihedral : 5.095 53.926 528 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.35 % Allowed : 20.22 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.84 (0.41), residues: 437 helix: 3.23 (0.31), residues: 262 sheet: 0.60 (0.68), residues: 57 loop : -0.73 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.008 0.001 TYR A 311 PHE 0.006 0.001 PHE B 94 TRP 0.011 0.001 TRP B 111 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3538) covalent geometry : angle 0.46460 ( 4817) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.15910 ( 2) hydrogen bonds : bond 0.03501 ( 235) hydrogen bonds : angle 3.54635 ( 693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.01 seconds wall clock time: 34 minutes 49.17 seconds (2089.17 seconds total)