Starting phenix.real_space_refine on Thu Jul 2 01:02:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lqt_63304/07_2026/9lqt_63304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lqt_63304/07_2026/9lqt_63304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lqt_63304/07_2026/9lqt_63304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lqt_63304/07_2026/9lqt_63304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lqt_63304/07_2026/9lqt_63304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lqt_63304/07_2026/9lqt_63304.map" } resolution = 2.6 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 42 5.16 5 C 3454 2.51 5 N 676 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4958 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2205 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2205 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 274 Unusual residues: {'CLR': 8, 'PCF': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 274 Unusual residues: {'CLR': 8, 'PCF': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 1.31, per 1000 atoms: 0.26 Number of scatterers: 4958 At special positions: 0 Unit cell: (66.03, 92.07, 77.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 2 15.00 O 784 8.00 N 676 7.00 C 3454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 181 " distance=2.04 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 181 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 209.4 milliseconds 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1084 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 85.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 29 through 55 Processing helix chain 'A' and resid 64 through 80 Processing helix chain 'A' and resid 81 through 91 Processing helix chain 'A' and resid 98 through 132 Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.421A pdb=" N ALA A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 Processing helix chain 'A' and resid 161 through 167 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 193 through 229 removed outlier: 5.150A pdb=" N VAL A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 245 through 278 Proline residue: A 263 - end of helix removed outlier: 3.550A pdb=" N MET A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 Proline residue: A 292 - end of helix removed outlier: 4.298A pdb=" N SER A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 313 removed outlier: 3.530A pdb=" N PHE A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'B' and resid 29 through 55 Processing helix chain 'B' and resid 64 through 80 Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 98 through 132 Processing helix chain 'B' and resid 133 through 144 removed outlier: 4.421A pdb=" N ALA B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 185 through 188 Processing helix chain 'B' and resid 193 through 229 removed outlier: 5.151A pdb=" N VAL B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Proline residue: B 213 - end of helix Processing helix chain 'B' and resid 245 through 278 Proline residue: B 263 - end of helix removed outlier: 3.549A pdb=" N MET B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 Proline residue: B 292 - end of helix removed outlier: 4.298A pdb=" N SER B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 313 removed outlier: 3.531A pdb=" N PHE B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 322 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 172 Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 172 358 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 640 1.30 - 1.42: 1354 1.42 - 1.55: 2885 1.55 - 1.68: 187 1.68 - 1.81: 64 Bond restraints: 5130 Sorted by residual: bond pdb=" C21 PCF A 401 " pdb=" O21 PCF A 401 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C21 PCF B 401 " pdb=" O21 PCF B 401 " ideal model delta sigma weight residual 1.334 1.434 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C31 PCF B 401 " pdb=" O31 PCF B 401 " ideal model delta sigma weight residual 1.329 1.407 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C31 PCF A 401 " pdb=" O31 PCF A 401 " ideal model delta sigma weight residual 1.329 1.407 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C21 PCF B 401 " pdb=" C22 PCF B 401 " ideal model delta sigma weight residual 1.503 1.571 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 5125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.10: 6990 5.10 - 10.20: 100 10.20 - 15.30: 2 15.30 - 20.40: 0 20.40 - 25.50: 2 Bond angle restraints: 7094 Sorted by residual: angle pdb=" O12 PCF B 401 " pdb=" P PCF B 401 " pdb=" O14 PCF B 401 " ideal model delta sigma weight residual 123.69 98.19 25.50 3.00e+00 1.11e-01 7.23e+01 angle pdb=" O12 PCF A 401 " pdb=" P PCF A 401 " pdb=" O14 PCF A 401 " ideal model delta sigma weight residual 123.69 98.20 25.49 3.00e+00 1.11e-01 7.22e+01 angle pdb=" C PHE A 101 " pdb=" N CYS A 102 " pdb=" CA CYS A 102 " ideal model delta sigma weight residual 120.68 113.81 6.87 1.70e+00 3.46e-01 1.63e+01 angle pdb=" C PHE B 101 " pdb=" N CYS B 102 " pdb=" CA CYS B 102 " ideal model delta sigma weight residual 120.68 113.82 6.86 1.70e+00 3.46e-01 1.63e+01 angle pdb=" C22 PCF A 401 " pdb=" C21 PCF A 401 " pdb=" O21 PCF A 401 " ideal model delta sigma weight residual 111.13 121.87 -10.74 3.00e+00 1.11e-01 1.28e+01 ... (remaining 7089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.84: 2980 11.84 - 23.67: 402 23.67 - 35.51: 204 35.51 - 47.35: 90 47.35 - 59.18: 56 Dihedral angle restraints: 3732 sinusoidal: 2058 harmonic: 1674 Sorted by residual: dihedral pdb=" CB CYS A 102 " pdb=" SG CYS A 102 " pdb=" SG CYS A 181 " pdb=" CB CYS A 181 " ideal model delta sinusoidal sigma weight residual 93.00 130.21 -37.21 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CB CYS B 102 " pdb=" SG CYS B 102 " pdb=" SG CYS B 181 " pdb=" CB CYS B 181 " ideal model delta sinusoidal sigma weight residual 93.00 130.20 -37.20 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA CYS B 181 " pdb=" C CYS B 181 " pdb=" N TYR B 182 " pdb=" CA TYR B 182 " ideal model delta harmonic sigma weight residual 180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 694 0.069 - 0.137: 100 0.137 - 0.206: 38 0.206 - 0.274: 32 0.274 - 0.343: 14 Chirality restraints: 878 Sorted by residual: chirality pdb=" C17 CLR B 406 " pdb=" C13 CLR B 406 " pdb=" C16 CLR B 406 " pdb=" C20 CLR B 406 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C17 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C16 CLR A 403 " pdb=" C20 CLR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C17 CLR B 403 " pdb=" C13 CLR B 403 " pdb=" C16 CLR B 403 " pdb=" C20 CLR B 403 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 875 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 174 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" CD GLU B 174 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU B 174 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU B 174 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 174 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" CD GLU A 174 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 174 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 174 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 313 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 314 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " -0.018 5.00e-02 4.00e+02 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1244 2.80 - 3.33: 4918 3.33 - 3.85: 8485 3.85 - 4.38: 10024 4.38 - 4.90: 17136 Nonbonded interactions: 41807 Sorted by model distance: nonbonded pdb=" NH1 ARG B 245 " pdb=" OD1 ASP B 313 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG A 245 " pdb=" OD1 ASP A 313 " model vdw 2.276 3.120 nonbonded pdb=" O SER A 193 " pdb=" OG SER A 193 " model vdw 2.276 3.040 nonbonded pdb=" O SER B 193 " pdb=" OG SER B 193 " model vdw 2.276 3.040 nonbonded pdb=" O LYS A 178 " pdb=" NE2 GLN A 180 " model vdw 2.358 3.120 ... (remaining 41802 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.290 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.010 0.101 5132 Z= 0.485 Angle : 1.366 25.505 7098 Z= 0.533 Chirality : 0.081 0.343 878 Planarity : 0.005 0.034 744 Dihedral : 15.707 59.185 2642 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 19.07 % Favored : 80.93 % 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: 1.78 (0.36), residues: 554 helix: 1.78 (0.24), residues: 450 sheet: -3.05 (1.01), residues: 20 loop : -0.89 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 133 TYR 0.011 0.001 TYR B 88 PHE 0.013 0.001 PHE A 101 TRP 0.007 0.001 TRP A 195 HIS 0.001 0.000 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.49 ( 5130) covalent geometry : angle 1.36376 / 0.53 ( 7094) SS BOND : bond 0.00834 / 0.42 ( 2) SS BOND : angle 3.80219 / 1.92 ( 4) hydrogen bonds : bond 0.13698 / 9.62 ( 358) hydrogen bonds : angle 5.43827 / 3.85 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.101 Fit side-chains REVERT: B 55 ARG cc_start: 0.6547 (ptt90) cc_final: 0.6297 (ptt90) REVERT: B 62 ARG cc_start: 0.7288 (mtm180) cc_final: 0.6802 (mpp80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.4646 time to fit residues: 35.2838 Evaluate side-chains 69 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.172806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131136 restraints weight = 4899.168| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.99 r_work: 0.3569 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5132 Z= 0.145 Angle : 0.700 8.066 7098 Z= 0.318 Chirality : 0.043 0.254 878 Planarity : 0.005 0.031 744 Dihedral : 13.177 59.927 1756 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.97 % Allowed : 13.77 % Favored : 83.26 % 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: 1.64 (0.35), residues: 554 helix: 1.68 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -1.92 (0.54), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 133 TYR 0.007 0.001 TYR B 293 PHE 0.009 0.001 PHE A 101 TRP 0.009 0.001 TRP B 195 HIS 0.001 0.001 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 5130) covalent geometry : angle 0.69645 / 0.32 ( 7094) SS BOND : bond 0.00712 / 0.36 ( 2) SS BOND : angle 2.89214 / 1.61 ( 4) hydrogen bonds : bond 0.04579 / 3.17 ( 358) hydrogen bonds : angle 4.33740 / 3.17 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.102 Fit side-chains REVERT: A 55 ARG cc_start: 0.6163 (ptt90) cc_final: 0.5832 (ptt90) REVERT: B 55 ARG cc_start: 0.6044 (ptt90) cc_final: 0.5715 (ptt90) REVERT: B 62 ARG cc_start: 0.7037 (mtm180) cc_final: 0.6321 (mpp80) REVERT: B 133 ARG cc_start: 0.5821 (mtt-85) cc_final: 0.5598 (mtp85) REVERT: B 159 LEU cc_start: 0.7741 (mt) cc_final: 0.7530 (mt) REVERT: B 301 ASN cc_start: 0.8526 (t0) cc_final: 0.8308 (t0) outliers start: 14 outliers final: 4 residues processed: 81 average time/residue: 0.4293 time to fit residues: 36.3546 Evaluate side-chains 77 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.0670 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN B 289 ASN B 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.175850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134762 restraints weight = 4805.296| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.95 r_work: 0.3525 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5132 Z= 0.126 Angle : 0.626 7.552 7098 Z= 0.291 Chirality : 0.041 0.240 878 Planarity : 0.004 0.031 744 Dihedral : 12.555 59.969 1756 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.75 % Allowed : 15.47 % Favored : 81.78 % 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: 1.91 (0.35), residues: 554 helix: 1.85 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.59 (0.53), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 133 TYR 0.009 0.001 TYR B 182 PHE 0.008 0.001 PHE B 78 TRP 0.006 0.001 TRP B 195 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 5130) covalent geometry : angle 0.62418 / 0.29 ( 7094) SS BOND : bond 0.00781 / 0.39 ( 2) SS BOND : angle 2.19773 / 1.20 ( 4) hydrogen bonds : bond 0.04059 / 2.81 ( 358) hydrogen bonds : angle 4.08107 / 3.01 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.100 Fit side-chains REVERT: A 55 ARG cc_start: 0.6137 (ptt90) cc_final: 0.5722 (ptt90) REVERT: B 55 ARG cc_start: 0.5917 (ptt90) cc_final: 0.5534 (ptt90) REVERT: B 62 ARG cc_start: 0.7057 (mtm180) cc_final: 0.6432 (mpp80) REVERT: B 159 LEU cc_start: 0.7583 (mt) cc_final: 0.7359 (mt) outliers start: 13 outliers final: 3 residues processed: 80 average time/residue: 0.4275 time to fit residues: 35.7414 Evaluate side-chains 72 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 227 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN B 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131366 restraints weight = 4837.680| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.98 r_work: 0.3574 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5132 Z= 0.138 Angle : 0.653 7.910 7098 Z= 0.302 Chirality : 0.042 0.255 878 Planarity : 0.004 0.031 744 Dihedral : 12.248 59.928 1756 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.60 % Allowed : 15.68 % Favored : 80.72 % 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: 1.99 (0.35), residues: 554 helix: 1.90 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.57 (0.53), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 133 TYR 0.008 0.001 TYR B 293 PHE 0.011 0.001 PHE B 101 TRP 0.007 0.001 TRP B 154 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 5130) covalent geometry : angle 0.64913 / 0.30 ( 7094) SS BOND : bond 0.00851 / 0.43 ( 2) SS BOND : angle 2.96841 / 1.56 ( 4) hydrogen bonds : bond 0.04228 / 2.92 ( 358) hydrogen bonds : angle 4.04975 / 2.98 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.167 Fit side-chains REVERT: A 55 ARG cc_start: 0.6198 (ptt90) cc_final: 0.5826 (ptt90) REVERT: B 55 ARG cc_start: 0.6041 (ptt90) cc_final: 0.5688 (ptt90) REVERT: B 159 LEU cc_start: 0.7769 (mt) cc_final: 0.7555 (mt) REVERT: B 180 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7485 (pm20) outliers start: 17 outliers final: 6 residues processed: 81 average time/residue: 0.4074 time to fit residues: 34.4880 Evaluate side-chains 75 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN B 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.173346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.131121 restraints weight = 4882.060| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.98 r_work: 0.3559 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5132 Z= 0.142 Angle : 0.653 7.853 7098 Z= 0.305 Chirality : 0.043 0.247 878 Planarity : 0.005 0.032 744 Dihedral : 11.808 59.882 1756 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.08 % Allowed : 13.98 % Favored : 80.93 % 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: 1.94 (0.35), residues: 554 helix: 1.86 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.58 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 244 TYR 0.007 0.001 TYR A 88 PHE 0.011 0.001 PHE B 101 TRP 0.009 0.001 TRP A 154 HIS 0.000 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5130) covalent geometry : angle 0.64942 / 0.30 ( 7094) SS BOND : bond 0.00782 / 0.40 ( 2) SS BOND : angle 2.98441 / 1.53 ( 4) hydrogen bonds : bond 0.04334 / 2.99 ( 358) hydrogen bonds : angle 4.04926 / 2.98 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.167 Fit side-chains REVERT: A 55 ARG cc_start: 0.6265 (ptt90) cc_final: 0.5882 (ptt90) REVERT: A 180 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: B 55 ARG cc_start: 0.6201 (ptt90) cc_final: 0.5855 (ptt90) outliers start: 24 outliers final: 11 residues processed: 82 average time/residue: 0.4494 time to fit residues: 38.5078 Evaluate side-chains 80 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.173441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131245 restraints weight = 4885.383| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.99 r_work: 0.3562 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5132 Z= 0.141 Angle : 0.656 7.727 7098 Z= 0.308 Chirality : 0.043 0.243 878 Planarity : 0.005 0.032 744 Dihedral : 11.678 59.762 1756 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.66 % Allowed : 14.41 % Favored : 80.93 % 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: 2.00 (0.35), residues: 554 helix: 1.91 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.60 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 244 TYR 0.007 0.001 TYR B 293 PHE 0.011 0.001 PHE B 101 TRP 0.009 0.001 TRP A 154 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 5130) covalent geometry : angle 0.65156 / 0.31 ( 7094) SS BOND : bond 0.00930 / 0.47 ( 2) SS BOND : angle 3.18461 / 1.65 ( 4) hydrogen bonds : bond 0.04282 / 2.96 ( 358) hydrogen bonds : angle 4.05221 / 2.98 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.108 Fit side-chains REVERT: A 55 ARG cc_start: 0.6243 (ptt90) cc_final: 0.5881 (ptt90) REVERT: A 180 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: B 55 ARG cc_start: 0.6214 (ptt90) cc_final: 0.5880 (ptt90) REVERT: B 180 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7485 (pm20) outliers start: 22 outliers final: 8 residues processed: 79 average time/residue: 0.4813 time to fit residues: 39.6615 Evaluate side-chains 78 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 43 optimal weight: 0.0470 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.176551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134415 restraints weight = 4737.097| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.79 r_work: 0.3491 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5132 Z= 0.121 Angle : 0.624 8.264 7098 Z= 0.295 Chirality : 0.041 0.229 878 Planarity : 0.004 0.031 744 Dihedral : 11.454 59.975 1756 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.18 % Allowed : 15.68 % Favored : 81.14 % 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: 2.15 (0.35), residues: 554 helix: 2.01 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.54 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 244 TYR 0.006 0.001 TYR B 185 PHE 0.009 0.001 PHE B 78 TRP 0.009 0.001 TRP A 154 HIS 0.000 0.000 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 5130) covalent geometry : angle 0.62140 / 0.29 ( 7094) SS BOND : bond 0.00804 / 0.40 ( 2) SS BOND : angle 2.52944 / 1.38 ( 4) hydrogen bonds : bond 0.03803 / 2.62 ( 358) hydrogen bonds : angle 3.96180 / 2.92 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.161 Fit side-chains REVERT: A 55 ARG cc_start: 0.6433 (ptt90) cc_final: 0.6086 (ptt90) REVERT: A 180 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: B 55 ARG cc_start: 0.6426 (ptt90) cc_final: 0.6093 (ptt90) outliers start: 15 outliers final: 3 residues processed: 82 average time/residue: 0.4591 time to fit residues: 39.3267 Evaluate side-chains 72 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.175994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.133891 restraints weight = 4709.299| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.78 r_work: 0.3479 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5132 Z= 0.127 Angle : 0.635 7.514 7098 Z= 0.303 Chirality : 0.042 0.234 878 Planarity : 0.004 0.031 744 Dihedral : 11.398 59.940 1756 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.54 % Allowed : 16.10 % Favored : 81.36 % 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: 2.18 (0.35), residues: 554 helix: 2.02 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.47 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 244 TYR 0.006 0.001 TYR B 293 PHE 0.009 0.001 PHE A 101 TRP 0.009 0.001 TRP A 154 HIS 0.001 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5130) covalent geometry : angle 0.63218 / 0.30 ( 7094) SS BOND : bond 0.00597 / 0.30 ( 2) SS BOND : angle 2.48908 / 1.34 ( 4) hydrogen bonds : bond 0.04006 / 2.77 ( 358) hydrogen bonds : angle 3.98850 / 2.94 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.175 Fit side-chains REVERT: A 55 ARG cc_start: 0.6420 (ptt90) cc_final: 0.6105 (ptt90) REVERT: B 55 ARG cc_start: 0.6424 (ptt90) cc_final: 0.6117 (ptt90) REVERT: B 289 ASN cc_start: 0.7854 (m110) cc_final: 0.7646 (m110) outliers start: 12 outliers final: 7 residues processed: 77 average time/residue: 0.5135 time to fit residues: 41.1718 Evaluate side-chains 76 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.181090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140386 restraints weight = 4781.005| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.87 r_work: 0.3624 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5132 Z= 0.138 Angle : 0.656 9.083 7098 Z= 0.310 Chirality : 0.043 0.234 878 Planarity : 0.004 0.031 744 Dihedral : 11.390 59.890 1756 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.18 % Allowed : 16.10 % Favored : 80.72 % 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: 2.14 (0.35), residues: 554 helix: 1.99 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.46 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 244 TYR 0.007 0.001 TYR B 293 PHE 0.011 0.001 PHE B 101 TRP 0.008 0.001 TRP A 154 HIS 0.000 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5130) covalent geometry : angle 0.65225 / 0.31 ( 7094) SS BOND : bond 0.00820 / 0.41 ( 2) SS BOND : angle 3.20178 / 1.67 ( 4) hydrogen bonds : bond 0.04152 / 2.87 ( 358) hydrogen bonds : angle 4.04605 / 2.98 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.163 Fit side-chains REVERT: A 55 ARG cc_start: 0.6258 (ptt90) cc_final: 0.5932 (ptt90) REVERT: B 55 ARG cc_start: 0.6247 (ptt90) cc_final: 0.5915 (ptt90) outliers start: 15 outliers final: 7 residues processed: 74 average time/residue: 0.4512 time to fit residues: 34.8858 Evaluate side-chains 76 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140710 restraints weight = 4798.761| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.88 r_work: 0.3628 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5132 Z= 0.135 Angle : 0.651 8.621 7098 Z= 0.311 Chirality : 0.043 0.232 878 Planarity : 0.004 0.031 744 Dihedral : 11.282 59.818 1756 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.54 % Allowed : 16.53 % Favored : 80.93 % 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: 2.14 (0.35), residues: 554 helix: 1.98 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.41 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 244 TYR 0.007 0.001 TYR B 293 PHE 0.010 0.001 PHE B 101 TRP 0.008 0.001 TRP A 154 HIS 0.000 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5130) covalent geometry : angle 0.64763 / 0.31 ( 7094) SS BOND : bond 0.00704 / 0.35 ( 2) SS BOND : angle 2.93879 / 1.56 ( 4) hydrogen bonds : bond 0.04139 / 2.86 ( 358) hydrogen bonds : angle 4.06383 / 3.00 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.165 Fit side-chains REVERT: A 55 ARG cc_start: 0.6267 (ptt90) cc_final: 0.5946 (ptt90) REVERT: B 55 ARG cc_start: 0.6303 (ptt90) cc_final: 0.5963 (ptt90) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.5188 time to fit residues: 39.4669 Evaluate side-chains 76 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140597 restraints weight = 4850.529| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.90 r_work: 0.3635 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5132 Z= 0.134 Angle : 0.660 10.599 7098 Z= 0.313 Chirality : 0.042 0.230 878 Planarity : 0.004 0.031 744 Dihedral : 11.213 58.567 1756 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.12 % Allowed : 17.16 % Favored : 80.72 % 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: 2.18 (0.35), residues: 554 helix: 2.01 (0.24), residues: 458 sheet: None (None), residues: 0 loop : -1.38 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 244 TYR 0.007 0.001 TYR B 293 PHE 0.010 0.001 PHE B 101 TRP 0.008 0.001 TRP B 154 HIS 0.000 0.000 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 5130) covalent geometry : angle 0.65612 / 0.31 ( 7094) SS BOND : bond 0.00778 / 0.39 ( 2) SS BOND : angle 2.94155 / 1.57 ( 4) hydrogen bonds : bond 0.04108 / 2.84 ( 358) hydrogen bonds : angle 4.06074 / 2.99 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1667.72 seconds wall clock time: 29 minutes 9.58 seconds (1749.58 seconds total)