Starting phenix.real_space_refine on Tue Mar 3 14:04:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i5n_52634/03_2026/9i5n_52634.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i5n_52634/03_2026/9i5n_52634.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/9i5n_52634/03_2026/9i5n_52634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i5n_52634/03_2026/9i5n_52634.map" model { file = "/net/cci-nas-00/data/ceres_data/9i5n_52634/03_2026/9i5n_52634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i5n_52634/03_2026/9i5n_52634.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= 0.026 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 Mg 1 5.21 5 S 14 5.16 5 C 1775 2.51 5 N 471 2.21 5 O 572 1.98 5 H 2763 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5596 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1756 Classifications: {'peptide': 118} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "A" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1620 Classifications: {'peptide': 107} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2180 Classifications: {'peptide': 143} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 136} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Classifications: {'water': 8} Link IDs: {None: 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASN C 119 " occ=0.00 ... (14 atoms not shown) pdb="HD22 ASN C 119 " occ=0.00 Time building chain proxies: 1.23, per 1000 atoms: 0.22 Number of scatterers: 5596 At special positions: 0 Unit cell: (64.7, 87.992, 73.758, 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 14 16.00 Mg 1 11.99 O 572 8.00 N 471 7.00 C 1775 6.00 H 2763 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.01 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 218 " 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: 0.28 Conformation dependent library (CDL) restraints added in 290.9 milliseconds 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 672 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.1% alpha, 40.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.651A pdb=" N ILE B 64 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.524A pdb=" N VAL A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.813A pdb=" N SER B 70 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 47 removed outlier: 3.820A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 38 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR B 109 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 47 removed outlier: 3.820A pdb=" N GLU B 46 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 38 " --> pdb=" O GLU B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'A' and resid 10 through 13 removed outlier: 5.935A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 102 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AA7, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.844A pdb=" N GLY C 167 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 179 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 153 through 156 removed outlier: 3.619A pdb=" N ASN C 240 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 189 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 208 " --> pdb=" O ALA C 191 " (cutoff:3.500A) 101 hydrogen bonds defined for protein. 246 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: 1.16 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 2762 1.12 - 1.29: 472 1.29 - 1.47: 1141 1.47 - 1.65: 1248 1.65 - 1.82: 21 Bond restraints: 5644 Sorted by residual: bond pdb=" CZ PHE B 27 " pdb=" HZ PHE B 27 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N SER A 49 " pdb=" H SER A 49 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N TYR C 172 " pdb=" H TYR C 172 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N SER A 7 " pdb=" H SER A 7 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" NE2 GLN B 86 " pdb="HE21 GLN B 86 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 5639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.23: 10102 7.23 - 14.45: 23 14.45 - 21.68: 0 21.68 - 28.90: 1 28.90 - 36.12: 2 Bond angle restraints: 10128 Sorted by residual: angle pdb=" N ASP A 30 " pdb=" CA ASP A 30 " pdb=" HA ASP A 30 " ideal model delta sigma weight residual 110.00 73.88 36.12 3.00e+00 1.11e-01 1.45e+02 angle pdb=" CA ASP A 30 " pdb=" CB ASP A 30 " pdb=" CG ASP A 30 " ideal model delta sigma weight residual 112.60 122.35 -9.75 1.00e+00 1.00e+00 9.51e+01 angle pdb=" C ASP A 30 " pdb=" CA ASP A 30 " pdb=" HA ASP A 30 " ideal model delta sigma weight residual 109.00 79.95 29.05 3.00e+00 1.11e-01 9.38e+01 angle pdb=" CB ASP A 30 " pdb=" CA ASP A 30 " pdb=" HA ASP A 30 " ideal model delta sigma weight residual 109.00 80.78 28.22 3.00e+00 1.11e-01 8.85e+01 angle pdb=" OE1 GLN B 6 " pdb=" CD GLN B 6 " pdb=" NE2 GLN B 6 " ideal model delta sigma weight residual 122.60 117.02 5.58 1.00e+00 1.00e+00 3.11e+01 ... (remaining 10123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 2357 17.06 - 34.12: 203 34.12 - 51.18: 86 51.18 - 68.23: 29 68.23 - 85.29: 15 Dihedral angle restraints: 2690 sinusoidal: 1447 harmonic: 1243 Sorted by residual: dihedral pdb=" C ASP A 30 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " pdb=" CB ASP A 30 " ideal model delta harmonic sigma weight residual -122.60 -139.84 17.24 0 2.50e+00 1.60e-01 4.75e+01 dihedral pdb=" N ASP A 30 " pdb=" C ASP A 30 " pdb=" CA ASP A 30 " pdb=" CB ASP A 30 " ideal model delta harmonic sigma weight residual 122.80 138.93 -16.13 0 2.50e+00 1.60e-01 4.16e+01 dihedral pdb=" CA ILE A 29 " pdb=" C ILE A 29 " pdb=" N ASP A 30 " pdb=" CA ASP A 30 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 2687 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 378 0.145 - 0.289: 52 0.289 - 0.433: 3 0.433 - 0.578: 0 0.578 - 0.722: 1 Chirality restraints: 434 Sorted by residual: chirality pdb=" CA ASP A 30 " pdb=" N ASP A 30 " pdb=" C ASP A 30 " pdb=" CB ASP A 30 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ASN A 52 " pdb=" N ASN A 52 " pdb=" C ASN A 52 " pdb=" CB ASN A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA PRO C 233 " pdb=" N PRO C 233 " pdb=" C PRO C 233 " pdb=" CB PRO C 233 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 431 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 140 " 0.440 2.00e-02 2.50e+03 1.47e-01 8.70e+02 pdb=" CG TRP C 140 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP C 140 " -0.118 2.00e-02 2.50e+03 pdb=" CD2 TRP C 140 " -0.109 2.00e-02 2.50e+03 pdb=" NE1 TRP C 140 " -0.162 2.00e-02 2.50e+03 pdb=" CE2 TRP C 140 " -0.074 2.00e-02 2.50e+03 pdb=" CE3 TRP C 140 " -0.118 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 140 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 140 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP C 140 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 TRP C 140 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP C 140 " -0.050 2.00e-02 2.50e+03 pdb=" HE3 TRP C 140 " -0.153 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 140 " 0.167 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 140 " -0.036 2.00e-02 2.50e+03 pdb=" HH2 TRP C 140 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 52 " -0.210 2.00e-02 2.50e+03 1.14e-01 5.16e+02 pdb=" CG TRP B 52 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 52 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 52 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP B 52 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 TRP B 52 " 0.071 2.00e-02 2.50e+03 pdb=" CE3 TRP B 52 " 0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 52 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 52 " 0.042 2.00e-02 2.50e+03 pdb=" CH2 TRP B 52 " -0.067 2.00e-02 2.50e+03 pdb=" HD1 TRP B 52 " -0.103 2.00e-02 2.50e+03 pdb=" HE1 TRP B 52 " 0.183 2.00e-02 2.50e+03 pdb=" HE3 TRP B 52 " 0.149 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 52 " -0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 52 " 0.028 2.00e-02 2.50e+03 pdb=" HH2 TRP B 52 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.062 2.00e-02 2.50e+03 6.57e-02 1.73e+02 pdb=" CG TRP B 47 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.085 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.081 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 47 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 47 " -0.164 2.00e-02 2.50e+03 pdb=" HE3 TRP B 47 " -0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 47 " 0.043 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 47 " -0.098 2.00e-02 2.50e+03 pdb=" HH2 TRP B 47 " -0.055 2.00e-02 2.50e+03 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 551 2.20 - 2.80: 10265 2.80 - 3.40: 15056 3.40 - 4.00: 20427 4.00 - 4.60: 30149 Nonbonded interactions: 76448 Sorted by model distance: nonbonded pdb=" OD2 ASP C 243 " pdb=" H1 HOH C 301 " model vdw 1.600 2.450 nonbonded pdb=" HG1 THR A 2 " pdb=" OD2 ASP A 28 " model vdw 1.609 2.450 nonbonded pdb=" O ILE B 69 " pdb=" H1 HOH B 201 " model vdw 1.613 2.450 nonbonded pdb="HH12 ARG A 61 " pdb=" OD2 ASP A 82 " model vdw 1.619 2.450 nonbonded pdb=" HG1 THR C 176 " pdb=" O PHE C 253 " model vdw 1.623 2.450 ... (remaining 76443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.590 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.045 2884 Z= 0.669 Angle : 1.862 10.759 3916 Z= 1.225 Chirality : 0.101 0.722 434 Planarity : 0.014 0.145 507 Dihedral : 15.361 85.292 1034 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.83 % Allowed : 5.52 % Favored : 93.65 % Rotamer: Outliers : 2.87 % Allowed : 12.10 % Favored : 85.03 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 17.65 % 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: -1.94 (0.41), residues: 362 helix: -2.72 (1.24), residues: 12 sheet: -1.03 (0.39), residues: 163 loop : -1.35 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 181 TYR 0.081 0.017 TYR A 67 PHE 0.089 0.017 PHE A 73 TRP 0.292 0.047 TRP C 140 HIS 0.015 0.006 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.01117 ( 2881) covalent geometry : angle 1.85927 ( 3910) SS BOND : bond 0.01450 ( 3) SS BOND : angle 3.17864 ( 6) hydrogen bonds : bond 0.21183 ( 91) hydrogen bonds : angle 11.08375 ( 246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 256 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6821 (t80) outliers start: 9 outliers final: 6 residues processed: 78 average time/residue: 0.0967 time to fit residues: 9.6678 Evaluate side-chains 72 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.190230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.172891 restraints weight = 10739.122| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.38 r_work: 0.4213 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4080 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2884 Z= 0.188 Angle : 0.690 5.793 3916 Z= 0.377 Chirality : 0.051 0.419 434 Planarity : 0.006 0.060 507 Dihedral : 8.775 57.136 407 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.08 % Favored : 93.65 % Rotamer: Outliers : 4.78 % Allowed : 15.61 % Favored : 79.62 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 17.65 % 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: 362 helix: -1.56 (1.64), residues: 12 sheet: -1.55 (0.35), residues: 178 loop : -1.43 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.011 0.002 TYR B 94 PHE 0.020 0.003 PHE B 80 TRP 0.016 0.002 TRP C 140 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2881) covalent geometry : angle 0.68762 ( 3910) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.67834 ( 6) hydrogen bonds : bond 0.04848 ( 91) hydrogen bonds : angle 8.48245 ( 246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7273 (m-30) cc_final: 0.6919 (m-30) REVERT: C 204 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7253 (tt) REVERT: C 256 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6795 (t80) outliers start: 15 outliers final: 12 residues processed: 78 average time/residue: 0.0902 time to fit residues: 9.1013 Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.190086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.172662 restraints weight = 10396.156| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.34 r_work: 0.4234 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.4105 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2884 Z= 0.136 Angle : 0.590 5.753 3916 Z= 0.320 Chirality : 0.050 0.420 434 Planarity : 0.005 0.039 507 Dihedral : 8.166 57.642 406 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.73 % Allowed : 16.88 % Favored : 77.39 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 17.65 % 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: -2.05 (0.41), residues: 362 helix: -1.39 (1.59), residues: 12 sheet: -1.33 (0.36), residues: 175 loop : -1.23 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.009 0.001 TYR B 94 PHE 0.013 0.002 PHE A 62 TRP 0.010 0.002 TRP B 110 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2881) covalent geometry : angle 0.58884 ( 3910) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.13764 ( 6) hydrogen bonds : bond 0.04019 ( 91) hydrogen bonds : angle 7.63015 ( 246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7095 (m-30) cc_final: 0.6890 (m-30) REVERT: C 256 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6763 (t80) outliers start: 18 outliers final: 15 residues processed: 77 average time/residue: 0.0888 time to fit residues: 8.9884 Evaluate side-chains 79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.187452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.169817 restraints weight = 10594.671| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.41 r_work: 0.4216 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2884 Z= 0.149 Angle : 0.580 5.149 3916 Z= 0.313 Chirality : 0.050 0.418 434 Planarity : 0.005 0.046 507 Dihedral : 8.055 57.173 406 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.41 % Allowed : 16.88 % Favored : 77.71 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 17.65 % 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: -2.13 (0.41), residues: 362 helix: -1.80 (1.58), residues: 12 sheet: -1.42 (0.36), residues: 175 loop : -1.22 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.012 0.001 TYR B 94 PHE 0.013 0.002 PHE A 62 TRP 0.010 0.002 TRP B 110 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 2881) covalent geometry : angle 0.57903 ( 3910) SS BOND : bond 0.00127 ( 3) SS BOND : angle 1.10030 ( 6) hydrogen bonds : bond 0.03737 ( 91) hydrogen bonds : angle 7.32791 ( 246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7103 (m-30) cc_final: 0.6873 (m-30) REVERT: C 256 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6786 (t80) outliers start: 17 outliers final: 15 residues processed: 72 average time/residue: 0.0834 time to fit residues: 7.9635 Evaluate side-chains 79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.188122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.171223 restraints weight = 10726.569| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 2.28 r_work: 0.4226 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2884 Z= 0.161 Angle : 0.576 5.374 3916 Z= 0.310 Chirality : 0.049 0.414 434 Planarity : 0.005 0.047 507 Dihedral : 7.966 56.326 406 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 6.69 % Allowed : 14.97 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.32 (0.40), residues: 362 helix: -1.59 (1.50), residues: 12 sheet: -1.64 (0.36), residues: 169 loop : -1.28 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.013 0.001 TYR B 94 PHE 0.014 0.002 PHE A 62 TRP 0.012 0.002 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2881) covalent geometry : angle 0.57490 ( 3910) SS BOND : bond 0.00192 ( 3) SS BOND : angle 1.04405 ( 6) hydrogen bonds : bond 0.03583 ( 91) hydrogen bonds : angle 7.04632 ( 246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7442 (m-30) cc_final: 0.7211 (m-30) REVERT: C 256 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6826 (t80) outliers start: 21 outliers final: 18 residues processed: 75 average time/residue: 0.0823 time to fit residues: 8.1386 Evaluate side-chains 81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.185810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.168237 restraints weight = 10703.885| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.41 r_work: 0.4210 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4076 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2884 Z= 0.176 Angle : 0.591 5.646 3916 Z= 0.318 Chirality : 0.049 0.416 434 Planarity : 0.005 0.047 507 Dihedral : 8.025 55.893 406 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.37 % Allowed : 14.65 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.48 (0.40), residues: 362 helix: -2.06 (1.45), residues: 12 sheet: -1.75 (0.36), residues: 169 loop : -1.37 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.014 0.002 TYR B 94 PHE 0.015 0.002 PHE B 80 TRP 0.011 0.002 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 2881) covalent geometry : angle 0.59010 ( 3910) SS BOND : bond 0.00154 ( 3) SS BOND : angle 1.08197 ( 6) hydrogen bonds : bond 0.03513 ( 91) hydrogen bonds : angle 6.99287 ( 246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7455 (m-30) cc_final: 0.7178 (m-30) REVERT: C 256 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6850 (t80) outliers start: 20 outliers final: 17 residues processed: 76 average time/residue: 0.0966 time to fit residues: 9.2310 Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.187389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.169920 restraints weight = 10666.849| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.41 r_work: 0.4223 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2884 Z= 0.141 Angle : 0.566 5.899 3916 Z= 0.302 Chirality : 0.049 0.417 434 Planarity : 0.005 0.040 507 Dihedral : 7.830 56.121 406 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.05 % Allowed : 15.61 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.29 (0.41), residues: 362 helix: -1.35 (1.64), residues: 12 sheet: -1.58 (0.35), residues: 174 loop : -1.30 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 181 TYR 0.011 0.001 TYR B 94 PHE 0.012 0.002 PHE B 80 TRP 0.010 0.002 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2881) covalent geometry : angle 0.56483 ( 3910) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.99413 ( 6) hydrogen bonds : bond 0.03323 ( 91) hydrogen bonds : angle 6.78209 ( 246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7433 (m-30) cc_final: 0.7193 (m-30) REVERT: C 256 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.6846 (t80) outliers start: 19 outliers final: 17 residues processed: 76 average time/residue: 0.0947 time to fit residues: 9.0535 Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.4457 r_free = 0.4457 target = 0.187408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.171225 restraints weight = 10451.212| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.19 r_work: 0.4246 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4121 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2884 Z= 0.139 Angle : 0.568 6.499 3916 Z= 0.303 Chirality : 0.049 0.416 434 Planarity : 0.006 0.081 507 Dihedral : 7.759 56.209 406 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.05 % Allowed : 15.29 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.22 (0.41), residues: 362 helix: -1.34 (1.63), residues: 12 sheet: -1.54 (0.35), residues: 174 loop : -1.25 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.012 0.001 TYR B 94 PHE 0.012 0.002 PHE A 62 TRP 0.010 0.001 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2881) covalent geometry : angle 0.56726 ( 3910) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.97771 ( 6) hydrogen bonds : bond 0.03259 ( 91) hydrogen bonds : angle 6.65503 ( 246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7571 (m-30) cc_final: 0.7292 (m-30) REVERT: A 82 ASP cc_start: 0.6252 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: C 256 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6877 (t80) outliers start: 19 outliers final: 16 residues processed: 75 average time/residue: 0.0941 time to fit residues: 9.0472 Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.180211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.163998 restraints weight = 10774.021| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.47 r_work: 0.4224 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2884 Z= 0.139 Angle : 0.568 6.951 3916 Z= 0.303 Chirality : 0.049 0.415 434 Planarity : 0.005 0.072 507 Dihedral : 7.692 56.701 406 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.73 % Allowed : 15.92 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.17 (0.41), residues: 362 helix: -1.21 (1.69), residues: 12 sheet: -1.49 (0.35), residues: 174 loop : -1.25 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 61 TYR 0.012 0.001 TYR B 94 PHE 0.011 0.002 PHE B 80 TRP 0.010 0.002 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2881) covalent geometry : angle 0.56721 ( 3910) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.97256 ( 6) hydrogen bonds : bond 0.03216 ( 91) hydrogen bonds : angle 6.56653 ( 246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7555 (m-30) cc_final: 0.7291 (m-30) REVERT: A 82 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.6104 (m-30) REVERT: C 256 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.6904 (t80) outliers start: 18 outliers final: 15 residues processed: 75 average time/residue: 0.0921 time to fit residues: 8.8083 Evaluate side-chains 77 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.181268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.164780 restraints weight = 10896.864| |-----------------------------------------------------------------------------| r_work (start): 0.4328 rms_B_bonded: 2.50 r_work: 0.4233 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2884 Z= 0.128 Angle : 0.561 6.922 3916 Z= 0.298 Chirality : 0.049 0.417 434 Planarity : 0.005 0.064 507 Dihedral : 7.265 56.859 403 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.41 % Allowed : 15.61 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.11 (0.42), residues: 362 helix: -1.17 (1.67), residues: 12 sheet: -1.45 (0.36), residues: 174 loop : -1.20 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 66 TYR 0.010 0.001 TYR B 94 PHE 0.011 0.002 PHE B 80 TRP 0.009 0.001 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2881) covalent geometry : angle 0.56012 ( 3910) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.96169 ( 6) hydrogen bonds : bond 0.03134 ( 91) hydrogen bonds : angle 6.46574 ( 246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 TYR cc_start: 0.7968 (m-80) cc_final: 0.7715 (m-80) REVERT: A 32 ASP cc_start: 0.7634 (m-30) cc_final: 0.7406 (m-30) REVERT: A 82 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.5985 (p0) REVERT: C 256 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.6896 (t80) outliers start: 17 outliers final: 15 residues processed: 72 average time/residue: 0.0964 time to fit residues: 8.9588 Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain C residue 178 CYS Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 256 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 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 = 0.4431 r_free = 0.4431 target = 0.184668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.167254 restraints weight = 10618.840| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.37 r_work: 0.4203 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4075 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2884 Z= 0.185 Angle : 0.603 6.750 3916 Z= 0.323 Chirality : 0.049 0.408 434 Planarity : 0.006 0.088 507 Dihedral : 7.545 55.723 403 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 5.41 % Allowed : 15.92 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -2.39 (0.41), residues: 362 helix: -1.21 (1.68), residues: 12 sheet: -1.72 (0.36), residues: 169 loop : -1.33 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 66 TYR 0.017 0.002 TYR B 94 PHE 0.017 0.002 PHE B 80 TRP 0.011 0.002 TRP B 110 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 2881) covalent geometry : angle 0.60198 ( 3910) SS BOND : bond 0.00113 ( 3) SS BOND : angle 1.01966 ( 6) hydrogen bonds : bond 0.03348 ( 91) hydrogen bonds : angle 6.64018 ( 246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.32 seconds wall clock time: 35 minutes 28.52 seconds (2128.52 seconds total)